chr11-2934936-T-C

Variant names:

• chr11-2934936-T-C
• rs2583442

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 0.264 in 152,064 control chromosomes in the GnomAD database, including 7,061 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 0.26 (7061 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40077 AN: 151948 Hom.: 7049 Cov.: 31

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.264 AC: 40097 AN: 152064 Hom.: 7061 Cov.: 31 AF XY: 0.268 AC XY: 19921 AN XY: 74322

African (AFR) AF: 0.0720 AC: 2990 AN: 41508

American (AMR) AF: 0.440 AC: 6715 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1254 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3475 AN: 5136

South Asian (SAS) AF: 0.398 AC: 1913 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2372 AN: 10584

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20155 AN: 67974

Other (OTH) AF: 0.310 AC: 655 AN: 2110

Alfa AF: 0.290 Hom.: 14517

Bravo AF: 0.273

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2583442; hg19: chr11-2956166; COSMIC: COSV68664258;