rs11101179

chr10-49602845-T-C

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 0.226 in 152,222 control chromosomes in the GnomAD database, including 4,946 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 0.23 (4946 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34362 AN: 152104 Hom.: 4947 Cov.: 33

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.226 AC: 34347 AN: 152222 Hom.: 4946 Cov.: 33 AF XY: 0.224 AC XY: 16649 AN XY: 74426

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.251

Alfa AF: 0.295 Hom.: 7096

Bravo AF: 0.213

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11101179; hg19: chr10-50810891;