rs11000122

Variant names:

• chr10-71962265-C-T
• rs11000122

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 0.25 in 151,474 control chromosomes in the GnomAD database, including 5,112 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 (5112 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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: 0.251 AC: 37922 AN: 151354 Hom.: 5104 Cov.: 29

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.250 AC: 37938 AN: 151474 Hom.: 5112 Cov.: 29 AF XY: 0.249 AC XY: 18400 AN XY: 73930

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.259

Alfa AF: 0.284 Hom.: 9502

Bravo AF: 0.246

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11000122; hg19: chr10-73722023;