rs10277011

Variant names:

• chr7-65441760-C-T
• rs10277011

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 0.249 in 151,918 control chromosomes in the GnomAD database, including 5,760 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 0.25 (5760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.249 AC: 37726 AN: 151800 Hom.: 5744 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.249 AC: 37762 AN: 151918 Hom.: 5760 Cov.: 32 AF XY: 0.248 AC XY: 18415 AN XY: 74256

African (AFR) AF: 0.392 AC: 16228 AN: 41404

American (AMR) AF: 0.345 AC: 5257 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5152

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10568

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11001 AN: 67968

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.195 Hom.: 1965

Bravo AF: 0.274

Asia WGS AF: 0.266 AC: 923 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10277011; hg19: chr7-64906673;