rs2313475

Variant names:

• chr13-20176637-G-A
• rs2313475

Your query was ambiguous. Multiple possible variants found:

• chr13-20176637-G-A
• chr13-20176637-G-C
• chr13-20176637-G-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 0.704 in 152,106 control chromosomes in the GnomAD database, including 38,621 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 0.70 (38621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.704 AC: 107045 AN: 151988 Hom.: 38601 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.704 AC: 107106 AN: 152106 Hom.: 38621 Cov.: 32 AF XY: 0.714 AC XY: 53111 AN XY: 74368

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.707

Alfa AF: 0.728 Hom.: 52519

Bravo AF: 0.695

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2313475; hg19: chr13-20750776;