Genetic Variant NM_014500.5:c.208A>G (chrX-136499619-A-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014500.5(HTATSF1):c.208A>G(p.Thr70Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 24)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

HTATSF1
NM_014500.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.32

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.20364454).

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.208A>G	p.Thr70Ala	missense	Exon 2 of 9	NP_055315.2
	HTATSF1	NM_001163280.2		c.208A>G	p.Thr70Ala	missense	Exon 3 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.208A>G	p.Thr70Ala	missense	Exon 2 of 9	ENSP00000218364.4	O43719
HTATSF1	ENST00000535601.5	TSL:1	c.208A>G	p.Thr70Ala	missense	Exon 3 of 10	ENSP00000442699.1	O43719
HTATSF1	ENST00000866998.1		c.208A>G	p.Thr70Ala	missense	Exon 2 of 9	ENSP00000537057.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1068420

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

345134

African (AFR)

AF:

0.00

AC:

AN:

24786

American (AMR)

AF:

0.00

AC:

AN:

27913

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18022

East Asian (EAS)

AF:

0.00

AC:

AN:

29395

South Asian (SAS)

AF:

0.00

AC:

AN:

48656

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39912

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4011

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

831011

Other (OTH)

AF:

0.00

AC:

AN:

44714

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.50

DEOGEN2

Benign

0.048

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.78

M_CAP

Benign

0.0040

MetaRNN

Benign

0.20

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

PhyloP100

4.3

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-0.67

REVEL

Benign

0.031

Sift

Benign

0.17

Sift4G

Benign

0.65

Polyphen

0.057

Vest4

0.21

MutPred

0.36

Loss of sheet (P = 0.0025)

MVP

0.56

MPC

0.49

ClinPred

0.63

GERP RS

4.4

Varity_R

0.12

gMVP

0.33

Mutation Taster

=84/16

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over