rs760760

chr6-15673945-T-C

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 0.2 in 152,182 control chromosomes in the GnomAD database, including 3,690 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 0.20 (3690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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 (EAS) allele frequency at 95% confidence interval = 0.462 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: 0.200 AC: 30418 AN: 152064 Hom.: 3681 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.200 AC: 30437 AN: 152182 Hom.: 3690 Cov.: 32 AF XY: 0.211 AC XY: 15723 AN XY: 74396

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.195

Alfa AF: 0.181 Hom.: 2680

Bravo AF: 0.200

Asia WGS AF: 0.352 AC: 1222 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	0.068
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760760; hg19: chr6-15674176;