rs10911193

Variant names:

• chr1-183021513-C-T
• rs10911193

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 0.113 in 152,170 control chromosomes in the GnomAD database, including 1,115 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 0.11 (1115 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 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: 0.113 AC: 17201 AN: 152052 Hom.: 1110 Cov.: 33

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.113 AC: 17225 AN: 152170 Hom.: 1115 Cov.: 33 AF XY: 0.116 AC XY: 8610 AN XY: 74380

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0856

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.115

Alfa AF: 0.119 Hom.: 150

Bravo AF: 0.122

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911193; hg19: chr1-182990648;