11-35075211-T-C

Variant names:

• chr11-35075211-T-C
• rs2553826

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 0.525 in 152,012 control chromosomes in the GnomAD database, including 21,567 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 0.53 (21567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.525 AC: 79802 AN: 151894 Hom.: 21561 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.525 AC: 79829 AN: 152012 Hom.: 21567 Cov.: 32 AF XY: 0.530 AC XY: 39370 AN XY: 74284

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.560

Alfa AF: 0.523 Hom.: 2546

Bravo AF: 0.524

Asia WGS AF: 0.686 AC: 2379 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2553826; hg19: chr11-35096758;