rs309762

chr4-176569411-A-Cchr4-176569411-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.908 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

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.901

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.10
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309762; hg19: chr4-177490562;