chr11-18272536-A-G

Variant names:

• chr11-18272536-A-G
• rs874957

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 0.392 in 152,078 control chromosomes in the GnomAD database, including 12,581 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 (12581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59518 AN: 151962 Hom.: 12547 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.392 AC: 59601 AN: 152078 Hom.: 12581 Cov.: 32 AF XY: 0.393 AC XY: 29233 AN XY: 74340

African (AFR) AF: 0.556 AC: 23070 AN: 41464

American (AMR) AF: 0.322 AC: 4927 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1188 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2066 AN: 5178

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4824

European-Finnish (FIN) AF: 0.404 AC: 4267 AN: 10564

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21101 AN: 67966

Other (OTH) AF: 0.371 AC: 786 AN: 2116

Alfa AF: 0.288 Hom.: 1494

Bravo AF: 0.394

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs874957; hg19: chr11-18294083;