rs2817460

Positions:

• chr6-156633907-T-A
• chr6-156633907-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 0.161 in 152,178 control chromosomes in the GnomAD database, including 2,208 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 0.16 (2208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 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: 0.161 AC: 24481 AN: 152060 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.161 AC: 24480 AN: 152178 Hom.: 2208 Cov.: 33 AF XY: 0.162 AC XY: 12017 AN XY: 74396

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0948 Hom.: 181

Bravo AF: 0.146

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.089
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: rs2817460; hg19: chr6-156955041; COSMIC: COSV60297138;