11-121213103-T-C

Variant names:

• chr11-121213103-T-C
• rs665035

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 0.658 in 152,092 control chromosomes in the GnomAD database, including 34,007 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 0.66 (34007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 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: 0.658 AC: 99990 AN: 151972 Hom.: 33961 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.658 AC: 100085 AN: 152092 Hom.: 34007 Cov.: 32 AF XY: 0.657 AC XY: 48822 AN XY: 74332

African (AFR) AF: 0.842 AC: 34961 AN: 41506

American (AMR) AF: 0.596 AC: 9097 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2906 AN: 5172

South Asian (SAS) AF: 0.576 AC: 2781 AN: 4828

European-Finnish (FIN) AF: 0.610 AC: 6438 AN: 10562

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39725 AN: 67964

Other (OTH) AF: 0.653 AC: 1380 AN: 2112

Alfa AF: 0.608 Hom.: 102471

Bravo AF: 0.665

Asia WGS AF: 0.563 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.65
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs665035; hg19: chr11-121083812;