10-118211822-T-C

Variant names:

• chr10-118211822-T-C
• rs703426

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 0.532 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.531 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

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.506

Alfa AF: 0.435 Hom.: 6980

Bravo AF: 0.558

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703426; hg19: chr10-119971334;