11-3638062-A-G

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 0.262 in 152,082 control chromosomes in the GnomAD database, including 8,863 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 0.26 (8863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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: 0.262 AC: 39804 AN: 151960 Hom.: 8819 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.262 AC: 39905 AN: 152082 Hom.: 8863 Cov.: 32 AF XY: 0.256 AC XY: 19069 AN XY: 74350

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.243

Alfa AF: 0.171 Hom.: 1467

Bravo AF: 0.288

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11028690; hg19: chr11-3659292;