11-636399-T-C

Position:

• chr11-636399-T-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 0.2 in 152,058 control chromosomes in the GnomAD database, including 3,152 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 0.20 (3152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30343 AN: 151940 Hom.: 3138 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.200 AC: 30401 AN: 152058 Hom.: 3152 Cov.: 32 AF XY: 0.207 AC XY: 15385 AN XY: 74346

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.212

Alfa AF: 0.186 Hom.: 3257

Bravo AF: 0.198

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758653; hg19: chr11-636399;