Variant 3-172497785-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.459 in 151,962 control chromosomes in the GnomAD database, including 16,299 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 0.46 ( 16299 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.184

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.459

AC:

69740

AN:

151844

Hom.:

16298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.418

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.363

Gnomad NFE

AF:

0.440

Gnomad OTH

AF:

0.457

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

GnomAD4 genome

AF:

0.459

AC:

69778

AN:

151962

Hom.:

16299

Cov.:

AF XY:

0.456

AC XY:

33860

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.529

Gnomad4 AMR

AF:

0.374

Gnomad4 ASJ

AF:

0.418

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.442

Gnomad4 NFE

AF:

0.440

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.437

Hom.:

19997

Bravo

AF:

0.457

Asia WGS

AF:

0.515

AC:

1788

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.8

DANN

Benign

0.70

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over