rs10271466

Variant names:

• chr7-10277135-A-G
• rs10271466

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 0.192 in 151,904 control chromosomes in the GnomAD database, including 3,024 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 0.19 (3024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.192 AC: 29154 AN: 151788 Hom.: 3021 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0562

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.192 AC: 29174 AN: 151904 Hom.: 3024 Cov.: 32 AF XY: 0.195 AC XY: 14478 AN XY: 74254

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.181

Alfa AF: 0.171 Hom.: 546

Bravo AF: 0.184

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10271466; hg19: chr7-10316762;