rs10271466

Variant names:

• chr7-10277135-A-G
• rs10271466

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 0.192 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.247 AC: 10240 AN: 41444

American (AMR) AF: 0.137 AC: 2085 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3464

East Asian (EAS) AF: 0.192 AC: 988 AN: 5146

South Asian (SAS) AF: 0.229 AC: 1106 AN: 4830

European-Finnish (FIN) AF: 0.271 AC: 2870 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10909 AN: 67902

Other (OTH) AF: 0.181 AC: 380 AN: 2102

Alfa AF: 0.170 Hom.: 876

Bravo AF: 0.184

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.59
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10271466; hg19: chr7-10316762;