11-76183085-C-T

Variant names:

• chr11-76183085-C-T
• rs663746

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;