chr11-55351315-C-T

Variant names:

• chr11-55351315-C-T
• rs72920657

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0272 in 152,100 control chromosomes in the GnomAD database, including 83 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 0.027 (83 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0272 (4135/152100) while in subpopulation NFE AF = 0.0403 (2738/67930). AF 95% confidence interval is 0.039. There are 83 homozygotes in GnomAd4. There are 1940 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 83 gene

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: 0.0272 AC: 4134 AN: 151982 Hom.: 83 Cov.: 33

Gnomad AFR AF: 0.00592

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0272 AC: 4135 AN: 152100 Hom.: 83 Cov.: 33 AF XY: 0.0261 AC XY: 1940 AN XY: 74326

African (AFR) AF: 0.00590 AC: 245 AN: 41540

American (AMR) AF: 0.0292 AC: 446 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.0186 AC: 90 AN: 4828

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0403 AC: 2738 AN: 67930

Other (OTH) AF: 0.0336 AC: 71 AN: 2110

Alfa AF: 0.0168 Hom.: 6

Bravo AF: 0.0273

Asia WGS AF: 0.00694 AC: 25 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.20
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs72920657; hg19: chr11-55118791;