rs3917365

Variant names:

• chr2-112828892-A-G
• rs3917365

Your query was ambiguous. Multiple possible variants found:

• chr2-112828892-A-G
• chr2-112828892-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 0.897 in 152,190 control chromosomes in the GnomAD database, including 61,467 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 0.90 (61467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

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 (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136482 AN: 152072 Hom.: 61419 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.897 AC: 136584 AN: 152190 Hom.: 61467 Cov.: 31 AF XY: 0.900 AC XY: 66963 AN XY: 74410

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.940

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.900

Alfa AF: 0.899 Hom.: 8124

Bravo AF: 0.896

Asia WGS AF: 0.921 AC: 3204 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	0.19
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: rs3917365; hg19: chr2-113586469;