11-636689-G-C

Position:

• chr11-636689-G-C

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 0.539 in 139,460 control chromosomes in the GnomAD database, including 19,471 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 (19471 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.539 AC: 75062 AN: 139340 Hom.: 19445 Cov.: 25

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.539 AC: 75142 AN: 139460 Hom.: 19471 Cov.: 25 AF XY: 0.540 AC XY: 36607 AN XY: 67778

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.538

Alfa AF: 0.392 Hom.: 1094

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747302; hg19: chr11-636689; COSMIC: COSV51562359;