dbSNP rs927340: HTATSF1P2:n.289C>T (chr6-3023484-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000604204.1(HTATSF1P2):n.289C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 156,968 control chromosomes in the GnomAD database, including 7,751 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.27 ( 7646 hom., cov: 33)

Exomes 𝑓: 0.20 ( 105 hom. )

Consequence

HTATSF1P2
ENST00000604204.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

19 publications found

Variant links:

Genes affected

HTATSF1P2 (HGNC:38586): (HIV-1 Tat specific factor 1 pseudogene 2)

HTATSF1P2 links:

ENSG00000288612 (HGNC:):

ENSG00000288612 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTATSF1P2	NR_033884.3 link	n.407C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HTATSF1P2	ENST00000604204.1 link	n.289C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000288612	ENST00000675225.1 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000288612	ENST00000676390.1 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41572

AN:

152046

Hom.:

7631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.469

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.239

GnomAD4 exome

AF:

0.198

AC:

951

AN:

4804

Hom.:

105

Cov.:

AF XY:

0.191

AC XY:

533

AN XY:

2786

show subpopulations

African (AFR)

AF:

0.594

AC:

114

AN:

192

American (AMR)

AF:

0.331

AC:

AN:

166

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

AN:

East Asian (EAS)

AF:

0.332

AC:

107

AN:

322

South Asian (SAS)

AF:

0.194

AC:

103

AN:

532

European-Finnish (FIN)

AF:

0.145

AC:

144

AN:

996

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.166

AC:

361

AN:

2178

Other (OTH)

AF:

0.166

AC:

AN:

350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

104

138

173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.274

AC:

41633

AN:

152164

Hom.:

7646

Cov.:

AF XY:

0.270

AC XY:

20083

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.517

AC:

21451

AN:

41474

American (AMR)

AF:

0.235

AC:

3591

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

431

AN:

3470

East Asian (EAS)

AF:

0.304

AC:

1571

AN:

5162

South Asian (SAS)

AF:

0.208

AC:

1002

AN:

4824

European-Finnish (FIN)

AF:

0.114

AC:

1214

AN:

10608

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11405

AN:

68014

Other (OTH)

AF:

0.238

AC:

502

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1402

2804

4205

5607

7009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.214

Hom.:

4580

Bravo

AF:

0.298

Asia WGS

AF:

0.255

AC:

886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.8

(source)

DANN

Benign

0.65

PhyloP100

-0.026

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over