rs760282

Variant names:

• chr17-42186274-A-G
• rs760282

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 0.342 in 151,890 control chromosomes in the GnomAD database, including 9,757 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 0.34 (9757 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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 = 0.516 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: 0.341 AC: 51830 AN: 151772 Hom.: 9733 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.342 AC: 51907 AN: 151890 Hom.: 9757 Cov.: 31 AF XY: 0.345 AC XY: 25637 AN XY: 74252

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.337

Alfa AF: 0.302 Hom.: 856

Bravo AF: 0.343

Asia WGS AF: 0.521 AC: 1805 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	1.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760282; hg19: chr17-40338292;