rs3917365

Variant names:

• chr2-112828892-A-G
• rs3917365
• ENST00000762706.1:n.405-56366A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-112828892-A-G
• chr2-112828892-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762706.1(ENSG00000299339):​n.405-56366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 16 publications found

Genes affected

ENSG00000299339 (HGNC:):

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 (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
ENSG00000299339	ENST00000762706.1	n.405-56366A>G		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.500-56366A>G		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.266-56366A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.823 AC: 34130 AN: 41468

American (AMR) AF: 0.936 AC: 14321 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3108 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5186

South Asian (SAS) AF: 0.869 AC: 4193 AN: 4826

European-Finnish (FIN) AF: 0.940 AC: 9957 AN: 10598

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62667 AN: 68026

Other (OTH) AF: 0.900 AC: 1901 AN: 2112

Alfa AF: 0.896 Hom.: 8382

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs3917365; hg19: chr2-113586469;