rs315946

Variant names:

• chr2-113136287-G-A
• rs315946

Your query was ambiguous. Multiple possible variants found:

• chr2-113136287-G-A
• chr2-113136287-G-C
• chr2-113136287-G-T

Variant summary

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

The variant allele was found at a frequency of 0.0941 in 152,124 control chromosomes in the GnomAD database, including 922 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 0.094 (922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.0943 AC: 14327 AN: 152006 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.0220

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0941 AC: 14320 AN: 152124 Hom.: 922 Cov.: 32 AF XY: 0.0913 AC XY: 6793 AN XY: 74364

African (AFR) AF: 0.0246 AC: 1021 AN: 41512

American (AMR) AF: 0.0664 AC: 1013 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0871 AC: 302 AN: 3466

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5180

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1303 AN: 10558

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10111 AN: 68000

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0938 Hom.: 558

Bravo AF: 0.0867

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs315946; hg19: chr2-113893864;