rs2136539

chr11-109169806-T-Achr11-109169806-T-Cchr11-109169806-T-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 0.894 in 152,088 control chromosomes in the GnomAD database, including 62,447 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 0.89 (62447 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 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: 0.895 AC: 135965 AN: 151970 Hom.: 62437 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.894 AC: 136018 AN: 152088 Hom.: 62447 Cov.: 31 AF XY: 0.899 AC XY: 66842 AN XY: 74334

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.899

Alfa AF: 0.945 Hom.: 3448

Bravo AF: 0.879

Asia WGS AF: 0.915 AC: 3181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.17
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2136539; hg19: chr11-109040533;