rs510317

Positions:

• chr13-113105440-A-G
• chr13-113105440-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 0.784 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.806

Alfa AF: 0.779 Hom.: 9228

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs510317; hg19: chr13-113759754;