rs7318115

Positions:

• chr13-60176687-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 0.702 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60176687A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.700

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7318115; hg19: chr13-60750821;