11-26874358-C-T

Variant names:

• chr11-26874358-C-T
• rs4431984

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 0.391 in 151,586 control chromosomes in the GnomAD database, including 11,850 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 0.39 (11850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.391 AC: 59216 AN: 151468 Hom.: 11842 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.391 AC: 59269 AN: 151586 Hom.: 11850 Cov.: 32 AF XY: 0.386 AC XY: 28621 AN XY: 74078

African (AFR) AF: 0.434 AC: 17908 AN: 41288

American (AMR) AF: 0.320 AC: 4870 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1589 AN: 3464

East Asian (EAS) AF: 0.223 AC: 1149 AN: 5152

South Asian (SAS) AF: 0.414 AC: 1987 AN: 4804

European-Finnish (FIN) AF: 0.367 AC: 3849 AN: 10500

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26723 AN: 67834

Other (OTH) AF: 0.397 AC: 835 AN: 2104

Alfa AF: 0.383 Hom.: 1859

Bravo AF: 0.386

Asia WGS AF: 0.346 AC: 1202 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.28
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4431984; hg19: chr11-26895905;