11-121213103-T-C

Variant names:

• chr11-121213103-T-C
• rs665035

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 0.658 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.653

Alfa AF: 0.596 Hom.: 40871

Bravo AF: 0.665

Asia WGS AF: 0.563 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665035; hg19: chr11-121083812;