11-76555128-C-T

Position:

• chr11-76555128-C-T

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 0.401 in 152,128 control chromosomes in the GnomAD database, including 12,647 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 0.40 (12647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

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: 0.401 AC: 60999 AN: 152010 Hom.: 12628 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.401 AC: 61041 AN: 152128 Hom.: 12647 Cov.: 32 AF XY: 0.402 AC XY: 29914 AN XY: 74362

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.404

Alfa AF: 0.422 Hom.: 2995

Bravo AF: 0.402

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2155220; hg19: chr11-76266172;