4-176569411-A-C

Variant names:

• chr4-176569411-A-C
• rs309762

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 0.908 in 152,250 control chromosomes in the GnomAD database, including 63,556 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 0.91 (63556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138128 AN: 152130 Hom.: 63516 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.908 AC: 138224 AN: 152250 Hom.: 63556 Cov.: 32 AF XY: 0.900 AC XY: 66994 AN XY: 74418

African (AFR) AF: 0.881 AC: 36606 AN: 41552

American (AMR) AF: 0.814 AC: 12452 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3288 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2544 AN: 5158

South Asian (SAS) AF: 0.878 AC: 4228 AN: 4818

European-Finnish (FIN) AF: 0.932 AC: 9885 AN: 10604

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66247 AN: 68024

Other (OTH) AF: 0.901 AC: 1901 AN: 2110

Alfa AF: 0.946 Hom.: 8491

Bravo AF: 0.895

Asia WGS AF: 0.690 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.31
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs309762; hg19: chr4-177490562;