rs3915080

Positions:

• chr3-22670018-A-G
• chr3-22670018-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 0.609 in 152,006 control chromosomes in the GnomAD database, including 28,277 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 0.61 (28277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92494 AN: 151888 Hom.: 28279 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.609 AC: 92531 AN: 152006 Hom.: 28277 Cov.: 32 AF XY: 0.608 AC XY: 45163 AN XY: 74282

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.602

Alfa AF: 0.616 Hom.: 11983

Bravo AF: 0.611

Asia WGS AF: 0.615 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3915080; hg19: chr3-22711509;