chr11-105994705-T-C

Variant names:

• chr11-105994705-T-C
• rs10895889

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 0.281 in 152,212 control chromosomes in the GnomAD database, including 5,998 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 0.28 (5998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42684 AN: 152096 Hom.: 5991 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.281 AC: 42723 AN: 152212 Hom.: 5998 Cov.: 33 AF XY: 0.282 AC XY: 20977 AN XY: 74408

African (AFR) AF: 0.282 AC: 11707 AN: 41548

American (AMR) AF: 0.259 AC: 3961 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5176

South Asian (SAS) AF: 0.264 AC: 1277 AN: 4830

European-Finnish (FIN) AF: 0.297 AC: 3143 AN: 10592

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19983 AN: 68000

Other (OTH) AF: 0.252 AC: 531 AN: 2106

Alfa AF: 0.292 Hom.: 792

Bravo AF: 0.273

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10895889; hg19: chr11-105865432;