11-2120356-C-T

Variant names:

• chr11-2120356-C-T
• rs6578987

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 0.714 in 152,142 control chromosomes in the GnomAD database, including 39,065 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 0.71 (39065 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.754 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: 0.714 AC: 108559 AN: 152024 Hom.: 39020 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.714 AC: 108665 AN: 152142 Hom.: 39065 Cov.: 33 AF XY: 0.711 AC XY: 52866 AN XY: 74366

African (AFR) AF: 0.743 AC: 30838 AN: 41514

American (AMR) AF: 0.766 AC: 11703 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2506 AN: 5160

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4822

European-Finnish (FIN) AF: 0.740 AC: 7841 AN: 10594

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48529 AN: 67988

Other (OTH) AF: 0.707 AC: 1491 AN: 2110

Alfa AF: 0.721 Hom.: 18485

Bravo AF: 0.722

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0020
DANN	Benign	0.55
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6578987; hg19: chr11-2141586;