Genetic Variant ENSG00000197462:n.389+40661T>C (chr7-125965048-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000769323.1(ENSG00000197462):n.389+40661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,796 control chromosomes in the GnomAD database, including 8,244 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 0.31 ( 8244 hom., cov: 32)

Consequence

ENSG00000197462
ENST00000769323.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.247

Publications

1 publications found

Variant links:

Genes affected

ENSG00000197462 (HGNC:):

ENSG00000197462 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000197462	ENST00000769323.1 link	n.389+40661T>C	intron_variant	Intron 2 of 2
ENSG00000197462	ENST00000769324.1 link	n.214+40661T>C	intron_variant	Intron 2 of 2
ENSG00000197462	ENST00000769325.1 link	n.310+40661T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47438

AN:

151676

Hom.:

8232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.443

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.411

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.361

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

GnomAD4 genome

AF:

0.313

AC:

47465

AN:

151796

Hom.:

8244

Cov.:

AF XY:

0.314

AC XY:

23285

AN XY:

74174

show subpopulations

African (AFR)

AF:

0.174

AC:

7232

AN:

41468

American (AMR)

AF:

0.485

AC:

7391

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

1537

AN:

3468

East Asian (EAS)

AF:

0.355

AC:

1835

AN:

5166

South Asian (SAS)

AF:

0.412

AC:

1985

AN:

4816

European-Finnish (FIN)

AF:

0.288

AC:

3044

AN:

10554

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.345

AC:

23372

AN:

67768

Other (OTH)

AF:

0.360

AC:

760

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1594

3189

4783

6378

7972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.309

Hom.:

1028

Bravo

AF:

0.323

Asia WGS

AF:

0.357

AC:

1239

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.7

(source)

DANN

Benign

0.68

PhyloP100

-0.25

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