11-76183085-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 0.439 in 152,134 control chromosomes in the GnomAD database, including 15,730 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 0.44 (15730 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.439 AC: 66717 AN: 152016 Hom.: 15721 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.439 AC: 66743 AN: 152134 Hom.: 15730 Cov.: 33 AF XY: 0.443 AC XY: 32922 AN XY: 74360

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.457

Alfa AF: 0.499 Hom.: 25338

Bravo AF: 0.437

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	14
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs663746; hg19: chr11-75894129;