11-80261501-C-T

Variant names:

• chr11-80261501-C-T
• rs1590087

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;