11-80261501-C-T

Position:

• chr11-80261501-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 0.588 in 151,934 control chromosomes in the GnomAD database, including 27,654 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 0.59 (27654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89232 AN: 151818 Hom.: 27603 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.588 AC: 89351 AN: 151934 Hom.: 27654 Cov.: 32 AF XY: 0.584 AC XY: 43325 AN XY: 74224

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.569

Alfa AF: 0.517 Hom.: 11470

Bravo AF: 0.611

Asia WGS AF: 0.514 AC: 1786 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1590087; hg19: chr11-79972545;