rs7319601

Variant names:

• chr13-20264080-G-A
• rs7319601

Your query was ambiguous. Multiple possible variants found:

• chr13-20264080-G-A
• chr13-20264080-G-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 0.345 in 151,936 control chromosomes in the GnomAD database, including 9,854 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 0.35 (9854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.47
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.346 AC: 52469 AN: 151818 Hom.: 9858 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.345 AC: 52469 AN: 151936 Hom.: 9854 Cov.: 32 AF XY: 0.345 AC XY: 25618 AN XY: 74232

African (AFR) AF: 0.181 AC: 7522 AN: 41454

American (AMR) AF: 0.392 AC: 5984 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2661 AN: 5142

South Asian (SAS) AF: 0.385 AC: 1848 AN: 4806

European-Finnish (FIN) AF: 0.399 AC: 4213 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27633 AN: 67934

Other (OTH) AF: 0.373 AC: 785 AN: 2102

Alfa AF: 0.389 Hom.: 6201

Bravo AF: 0.340

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.010
DANN	Benign	0.31
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs7319601; hg19: chr13-20838219;