rs2136539

Variant names:

• chr11-109169806-T-A
• rs2136539

Your query was ambiguous. Multiple possible variants found:

• chr11-109169806-T-A
• chr11-109169806-T-C
• chr11-109169806-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;