11-18256551-T-G

Variant names:

• chr11-18256551-T-G
• rs2045272

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 0.415 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
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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

African (AFR) AF: 0.346 AC: 14267 AN: 41248

American (AMR) AF: 0.435 AC: 6616 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1214 AN: 5140

South Asian (SAS) AF: 0.308 AC: 1476 AN: 4788

European-Finnish (FIN) AF: 0.434 AC: 4523 AN: 10422

Middle Eastern (MID) AF: 0.306 AC: 88 AN: 288

European-Non Finnish (NFE) AF: 0.476 AC: 32325 AN: 67856

Other (OTH) AF: 0.383 AC: 806 AN: 2104

Alfa AF: 0.439 Hom.: 64477

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2045272; hg19: chr11-18278098;