10-118211822-T-C

Variant names:

• chr10-118211822-T-C
• rs703426

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 0.532 in 151,916 control chromosomes in the GnomAD database, including 23,111 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 0.53 (23111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 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: 0.531 AC: 80646 AN: 151800 Hom.: 23070 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.532 AC: 80745 AN: 151916 Hom.: 23111 Cov.: 31 AF XY: 0.534 AC XY: 39652 AN XY: 74252

African (AFR) AF: 0.713 AC: 29519 AN: 41404

American (AMR) AF: 0.581 AC: 8866 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1688 AN: 3472

East Asian (EAS) AF: 0.861 AC: 4462 AN: 5180

South Asian (SAS) AF: 0.413 AC: 1984 AN: 4808

European-Finnish (FIN) AF: 0.414 AC: 4367 AN: 10540

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28161 AN: 67946

Other (OTH) AF: 0.506 AC: 1069 AN: 2112

Alfa AF: 0.434 Hom.: 7692

Bravo AF: 0.558

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs703426; hg19: chr10-119971334;