rs11195417

Variant names:

• chr10-111072236-C-A
• rs11195417

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 0.159 in 152,102 control chromosomes in the GnomAD database, including 2,552 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 (2552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.159 AC: 24224 AN: 151984 Hom.: 2551 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.159 AC: 24241 AN: 152102 Hom.: 2552 Cov.: 31 AF XY: 0.157 AC XY: 11659 AN XY: 74372

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.0946

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.137

Alfa AF: 0.114 Hom.: 1899

Bravo AF: 0.164

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11195417; hg19: chr10-112831994;