rs2317446

Positions:

• chr13-112620363-C-A

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 0.0936 in 150,766 control chromosomes in the GnomAD database, including 949 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 (949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14090 AN: 150648 Hom.: 948 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0936 AC: 14113 AN: 150766 Hom.: 949 Cov.: 31 AF XY: 0.0962 AC XY: 7090 AN XY: 73674

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0492 Hom.: 533

Bravo AF: 0.0964

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.039
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317446; hg19: chr13-113274677;