11-56128269-G-T

Variant names:

• chr11-56128269-G-T
• rs2220004

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 0.3 in 151,534 control chromosomes in the GnomAD database, including 7,108 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 0.30 (7108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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: 0.300 AC: 45493 AN: 151414 Hom.: 7106 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.300 AC: 45505 AN: 151534 Hom.: 7108 Cov.: 32 AF XY: 0.294 AC XY: 21756 AN XY: 74072

African (AFR) AF: 0.273 AC: 11312 AN: 41376

American (AMR) AF: 0.300 AC: 4552 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1447 AN: 3454

East Asian (EAS) AF: 0.149 AC: 773 AN: 5172

South Asian (SAS) AF: 0.206 AC: 991 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2487 AN: 10518

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22759 AN: 67698

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.228 Hom.: 724

Bravo AF: 0.306

Asia WGS AF: 0.162 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.33
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2220004; hg19: chr11-55895745; COSMIC: COSV57911379;