rs2317446

Variant names:

• chr13-112620363-C-A
• rs2317446

Your query was ambiguous. Multiple possible variants found:

• chr13-112620363-C-A
• chr13-112620363-C-G
• chr13-112620363-C-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 0.0936 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.180 AC: 7282 AN: 40348

American (AMR) AF: 0.121 AC: 1832 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3468

East Asian (EAS) AF: 0.0791 AC: 408 AN: 5156

South Asian (SAS) AF: 0.0475 AC: 229 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1288 AN: 10542

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0409 AC: 2780 AN: 67970

Other (OTH) AF: 0.0872 AC: 181 AN: 2076

Alfa AF: 0.0557 Hom.: 1551

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2317446; hg19: chr13-113274677;