rs3910516

Positions:

• chr2-215438330-A-G
• chr2-215438330-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 0.785 in 150,142 control chromosomes in the GnomAD database, including 46,748 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 0.79 (46748 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.785 AC: 117841 AN: 150040 Hom.: 46710 Cov.: 26

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.785 AC: 117923 AN: 150142 Hom.: 46748 Cov.: 26 AF XY: 0.787 AC XY: 57669 AN XY: 73238

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.780

Alfa AF: 0.764 Hom.: 3830

Bravo AF: 0.793

Asia WGS AF: 0.701 AC: 2427 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3910516; hg19: chr2-216303053;