rs510317

Variant names:

• chr13-113105440-A-G
• rs510317

Your query was ambiguous. Multiple possible variants found:

• chr13-113105440-A-G
• chr13-113105440-A-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 0.784 in 152,116 control chromosomes in the GnomAD database, including 47,205 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 0.78 (47205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.784 AC: 119169 AN: 151998 Hom.: 47164 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.784 AC: 119259 AN: 152116 Hom.: 47205 Cov.: 32 AF XY: 0.780 AC XY: 57989 AN XY: 74338

African (AFR) AF: 0.863 AC: 35791 AN: 41496

American (AMR) AF: 0.741 AC: 11325 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3208 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2858 AN: 5166

South Asian (SAS) AF: 0.846 AC: 4082 AN: 4826

European-Finnish (FIN) AF: 0.678 AC: 7167 AN: 10574

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52206 AN: 67992

Other (OTH) AF: 0.806 AC: 1695 AN: 2104

Alfa AF: 0.780 Hom.: 15915

Bravo AF: 0.785

Asia WGS AF: 0.702 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.26
PhyloP100		-1.5
PromoterAI		-0.0096	Neutral

Splicing

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

Other links and lift over

dbSNP: rs510317; hg19: chr13-113759754;