11-1209163-C-T

Variant names:

• chr11-1209163-C-T
• rs34595903

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 0.249 in 152,150 control chromosomes in the GnomAD database, including 5,714 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 0.25 (5714 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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: 0.249 AC: 37899 AN: 152032 Hom.: 5715 Cov.: 33

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.249 AC: 37891 AN: 152150 Hom.: 5714 Cov.: 33 AF XY: 0.251 AC XY: 18697 AN XY: 74364

African (AFR) AF: 0.0793 AC: 3295 AN: 41538

American (AMR) AF: 0.243 AC: 3715 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2576 AN: 5148

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3517 AN: 10586

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20974 AN: 67968

Other (OTH) AF: 0.273 AC: 577 AN: 2114

Alfa AF: 0.247 Hom.: 1904

Bravo AF: 0.235

Asia WGS AF: 0.353 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.72
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs34595903; hg19: chr11-1230393;