11-121213103-T-C

Position:

• chr11-121213103-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;