rs11190179

Variant names:

• chr10-99605556-G-A
• rs11190179

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 0.102 in 152,172 control chromosomes in the GnomAD database, including 981 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 0.10 (981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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: 0.102 AC: 15530 AN: 152054 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.102 AC: 15532 AN: 152172 Hom.: 981 Cov.: 32 AF XY: 0.105 AC XY: 7792 AN XY: 74390

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0984

Alfa AF: 0.108 Hom.: 1986

Bravo AF: 0.100

Asia WGS AF: 0.216 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11190179; hg19: chr10-101365313;