4-179743500-A-G

Variant names:

• chr4-179743500-A-G
• rs2383393

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.65 in 151,750 control chromosomes in the GnomAD database, including 32,524 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 0.65 (32524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98502 AN: 151632 Hom.: 32479 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.650 AC: 98605 AN: 151750 Hom.: 32524 Cov.: 32 AF XY: 0.651 AC XY: 48264 AN XY: 74134

African (AFR) AF: 0.723 AC: 29971 AN: 41430

American (AMR) AF: 0.654 AC: 9959 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2034 AN: 3462

East Asian (EAS) AF: 0.843 AC: 4357 AN: 5168

South Asian (SAS) AF: 0.690 AC: 3323 AN: 4818

European-Finnish (FIN) AF: 0.530 AC: 5589 AN: 10546

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41181 AN: 67782

Other (OTH) AF: 0.667 AC: 1406 AN: 2108

Alfa AF: 0.623 Hom.: 61796

Bravo AF: 0.662

Asia WGS AF: 0.740 AC: 2562 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2383393; hg19: chr4-180664653;