chr11-43055939-C-T

Variant names:

• chr11-43055939-C-T
• rs2042684

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 0.653 in 152,094 control chromosomes in the GnomAD database, including 32,537 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 0.65 (32537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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: 0.653 AC: 99296 AN: 151976 Hom.: 32516 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.653 AC: 99364 AN: 152094 Hom.: 32537 Cov.: 33 AF XY: 0.653 AC XY: 48567 AN XY: 74332

African (AFR) AF: 0.659 AC: 27306 AN: 41462

American (AMR) AF: 0.677 AC: 10343 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3701 AN: 5170

South Asian (SAS) AF: 0.707 AC: 3408 AN: 4820

European-Finnish (FIN) AF: 0.638 AC: 6744 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43597 AN: 68004

Other (OTH) AF: 0.657 AC: 1385 AN: 2108

Alfa AF: 0.649 Hom.: 5923

Bravo AF: 0.654

Asia WGS AF: 0.686 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2042684; hg19: chr11-43077489;