11-18256551-T-G

Variant names:

• chr11-18256551-T-G
• rs2045272

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 0.415 in 151,450 control chromosomes in the GnomAD database, including 13,399 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 0.41 (13399 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 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: 0.415 AC: 62738 AN: 151354 Hom.: 13386 Cov.: 29

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.415 AC: 62783 AN: 151450 Hom.: 13399 Cov.: 29 AF XY: 0.410 AC XY: 30358 AN XY: 73974

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.383

Alfa AF: 0.438 Hom.: 29113

Bravo AF: 0.410

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2045272; hg19: chr11-18278098;