rs7318115

Variant names:

• chr13-60176687-A-T
• rs7318115

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 0.702 in 152,050 control chromosomes in the GnomAD database, including 37,519 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 0.70 (37519 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.717 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: 0.702 AC: 106640 AN: 151928 Hom.: 37478 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.702 AC: 106737 AN: 152050 Hom.: 37519 Cov.: 31 AF XY: 0.698 AC XY: 51882 AN XY: 74312

African (AFR) AF: 0.701 AC: 29053 AN: 41468

American (AMR) AF: 0.708 AC: 10821 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2469 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2928 AN: 5166

South Asian (SAS) AF: 0.678 AC: 3262 AN: 4812

European-Finnish (FIN) AF: 0.654 AC: 6913 AN: 10564

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49084 AN: 67974

Other (OTH) AF: 0.700 AC: 1477 AN: 2110

Alfa AF: 0.713 Hom.: 4790

Bravo AF: 0.705

Asia WGS AF: 0.605 AC: 2108 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	3.3
DANN	Benign	0.45
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs7318115; hg19: chr13-60750821;