dbSNP rs847964: ENSG00000295809:n.87+17170C>T (chr7-12453831-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 ENST00000732860.1(ENSG00000295809):n.87+17170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,942 control chromosomes in the GnomAD database, including 985 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 0.10 ( 985 hom., cov: 32)

Consequence

ENSG00000295809
ENST00000732860.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Publications

0 publications found

Variant links:

Genes affected

ENSG00000295809 (HGNC:):

ENSG00000295809 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=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295809	ENST00000732860.1 link	n.87+17170C>T		intron_variant	Intron 1 of 2
ENSG00000295809	ENST00000732861.1 link	n.133+5054C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15540

AN:

151824

Hom.:

978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.0943

Gnomad EAS

AF:

0.0615

Gnomad SAS

AF:

0.0426

Gnomad FIN

AF:

0.0389

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0773

Gnomad OTH

AF:

0.104

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.102

AC:

15568

AN:

151942

Hom.:

985

Cov.:

AF XY:

0.0996

AC XY:

7392

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.177

AC:

7313

AN:

41412

American (AMR)

AF:

0.0843

AC:

1286

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0943

AC:

327

AN:

3466

East Asian (EAS)

AF:

0.0613

AC:

317

AN:

5172

South Asian (SAS)

AF:

0.0424

AC:

204

AN:

4812

European-Finnish (FIN)

AF:

0.0389

AC:

410

AN:

10552

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0773

AC:

5254

AN:

67964

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

679

1359

2038

2718

3397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.0897

Hom.:

Bravo

AF:

0.111

Asia WGS

AF:

0.0620

AC:

216

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.12

(source)

DANN

Benign

0.085

PhyloP100

-1.7

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over