dbSNP rs147796802: HTATSF1:p.Asp147Asp (chrX-136500689-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_014500.5(HTATSF1):c.441T>C(p.Asp147Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,146,759 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 47 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00071 ( 0 hom., 21 hem., cov: 24)

Exomes 𝑓: 0.000095 ( 0 hom. 26 hem. )

Consequence

HTATSF1
NM_014500.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.498

Publications

1 publications found

Variant links:

Genes affected

HTATSF1 (HGNC:5276): (HIV-1 Tat specific factor 1) The protein encoded by this gene functions as a cofactor for the stimulation of transcriptional elongation by HIV-1 Tat, which binds to the HIV-1 promoter through Tat-TAR interaction. This protein may also serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Sep 2009]

HTATSF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant X-136500689-T-C is Benign according to our data. Variant chrX-136500689-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2661520.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.498 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 21 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014500.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTATSF1	NM_014500.5	MANE Select	c.441T>C	p.Asp147Asp	synonymous	Exon 4 of 9	NP_055315.2
	HTATSF1	NM_001163280.2		c.441T>C	p.Asp147Asp	synonymous	Exon 5 of 10	NP_001156752.1	O43719

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
HTATSF1	ENST00000218364.5	TSL:1 MANE Select	c.441T>C	p.Asp147Asp	synonymous	Exon 4 of 9	ENSP00000218364.4	O43719
HTATSF1	ENST00000535601.5	TSL:1	c.441T>C	p.Asp147Asp	synonymous	Exon 5 of 10	ENSP00000442699.1	O43719
HTATSF1	ENST00000866998.1		c.441T>C	p.Asp147Asp	synonymous	Exon 4 of 9	ENSP00000537057.1

Frequencies

GnomAD3 genomes

AF:

0.000710

AC:

AN:

112662

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00229

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000562

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00422

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00131

GnomAD2 exomes

AF:

0.000214

AC:

AN:

140455

AF XY:

0.000150

show subpopulations

Gnomad AFR exome

AF:

0.00264

Gnomad AMR exome

AF:

0.000134

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000948

AC:

AN:

1034045

Hom.:

Cov.:

AF XY:

0.0000799

AC XY:

AN XY:

325229

show subpopulations

African (AFR)

AF:

0.00373

AC:

AN:

22765

American (AMR)

AF:

0.000130

AC:

AN:

23002

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17779

East Asian (EAS)

AF:

0.00

AC:

AN:

27773

South Asian (SAS)

AF:

0.00

AC:

AN:

44445

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39899

Middle Eastern (MID)

AF:

0.000758

AC:

AN:

3960

European-Non Finnish (NFE)

AF:

0.00000123

AC:

AN:

811017

Other (OTH)

AF:

0.000138

AC:

AN:

43405

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000710

AC:

AN:

112714

Hom.:

Cov.:

AF XY:

0.000602

AC XY:

AN XY:

34878

show subpopulations

African (AFR)

AF:

0.00229

AC:

AN:

31069

American (AMR)

AF:

0.000561

AC:

AN:

10698

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2651

East Asian (EAS)

AF:

0.00

AC:

AN:

3618

South Asian (SAS)

AF:

0.00

AC:

AN:

2765

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6175

Middle Eastern (MID)

AF:

0.00465

AC:

AN:

215

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53292

Other (OTH)

AF:

0.00130

AC:

AN:

1544

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000569

Hom.:

Bravo

AF:

0.000722

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

7.7

(source)

DANN

Benign

0.55

PhyloP100

0.50

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=93/7

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over