11-55351315-C-T

Position:

• chr11-55351315-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 83 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00590

Gnomad4 AMR AF: 0.0292

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0186

Gnomad4 FIN AF: 0.0278

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.0336

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72920657; hg19: chr11-55118791;