rs10282088

Variant names:

• chr7-45910847-C-A
• rs10282088

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 0.164 in 151,750 control chromosomes in the GnomAD database, including 2,286 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 (2286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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: 0.164 AC: 24808 AN: 151630 Hom.: 2284 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.164 AC: 24812 AN: 151750 Hom.: 2286 Cov.: 32 AF XY: 0.161 AC XY: 11952 AN XY: 74160

African (AFR) AF: 0.143 AC: 5930 AN: 41382

American (AMR) AF: 0.194 AC: 2955 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3460

East Asian (EAS) AF: 0.332 AC: 1704 AN: 5136

South Asian (SAS) AF: 0.113 AC: 542 AN: 4786

European-Finnish (FIN) AF: 0.0984 AC: 1040 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11677 AN: 67880

Other (OTH) AF: 0.189 AC: 397 AN: 2102

Alfa AF: 0.172 Hom.: 8894

Bravo AF: 0.175

Asia WGS AF: 0.214 AC: 739 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.50
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10282088; hg19: chr7-45950446;