rs760760

Variant names:

• chr6-15673945-T-C
• rs760760

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 0.2 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.135 AC: 5617 AN: 41530

American (AMR) AF: 0.317 AC: 4846 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2478 AN: 5184

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4820

European-Finnish (FIN) AF: 0.324 AC: 3422 AN: 10572

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11677 AN: 67994

Other (OTH) AF: 0.195 AC: 413 AN: 2114

Alfa AF: 0.185 Hom.: 8247

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs760760; hg19: chr6-15674176;