11-2179933-T-C

Variant names:

• chr11-2179933-T-C
• rs6578993

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 0.85 in 152,110 control chromosomes in the GnomAD database, including 55,119 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 0.85 (55119 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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 = 0.908 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: 0.850 AC: 129127 AN: 151992 Hom.: 55068 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.850 AC: 129239 AN: 152110 Hom.: 55119 Cov.: 31 AF XY: 0.848 AC XY: 63023 AN XY: 74348

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.851

Alfa AF: 0.834 Hom.: 51482

Bravo AF: 0.849

Asia WGS AF: 0.854 AC: 2972 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	2.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6578993; hg19: chr11-2201163;