11-105577727-T-C

Variant names:

• chr11-105577727-T-C
• rs10895837

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.806 in 152,042 control chromosomes in the GnomAD database, including 50,596 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 0.81 (50596 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122475 AN: 151924 Hom.: 50588 Cov.: 33

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.806 AC: 122528 AN: 152042 Hom.: 50596 Cov.: 33 AF XY: 0.808 AC XY: 60047 AN XY: 74342

African (AFR) AF: 0.604 AC: 25040 AN: 41444

American (AMR) AF: 0.866 AC: 13198 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3055 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4379 AN: 5194

South Asian (SAS) AF: 0.849 AC: 4104 AN: 4832

European-Finnish (FIN) AF: 0.892 AC: 9466 AN: 10614

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60535 AN: 67924

Other (OTH) AF: 0.816 AC: 1722 AN: 2110

Alfa AF: 0.860 Hom.: 69212

Bravo AF: 0.793

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10895837; hg19: chr11-105448454;