11-18272536-A-G

Variant names:

• chr11-18272536-A-G
• rs874957

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.392 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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.371

Alfa AF: 0.280 Hom.: 1358

Bravo AF: 0.394

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874957; hg19: chr11-18294083;