11-117880025-C-G

Variant names:

• chr11-117880025-C-G
• rs497768

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 0.538 in 151,876 control chromosomes in the GnomAD database, including 22,282 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 0.54 (22282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.538 AC: 81651 AN: 151758 Hom.: 22283 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.538 AC: 81679 AN: 151876 Hom.: 22282 Cov.: 31 AF XY: 0.532 AC XY: 39441 AN XY: 74196

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.555

Alfa AF: 0.552 Hom.: 2932

Bravo AF: 0.539

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs497768; hg19: chr11-117750740;