11-118873063-T-C

Variant names:

• chr11-118873063-T-C
• rs6421571

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 0.794 in 152,140 control chromosomes in the GnomAD database, including 48,022 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 0.79 (48022 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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: 0.794 AC: 120694 AN: 152022 Hom.: 47990 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.794 AC: 120779 AN: 152140 Hom.: 48022 Cov.: 32 AF XY: 0.797 AC XY: 59305 AN XY: 74384

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.818

Alfa AF: 0.805 Hom.: 69773

Bravo AF: 0.794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.019
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6421571; hg19: chr11-118743772;