rs2137111

chr15-77559193-G-A

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 151,978 control chromosomes in the GnomAD database, including 3,352 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 (3352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 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: 0.200 AC: 30405 AN: 151858 Hom.: 3353 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.200 AC: 30403 AN: 151978 Hom.: 3352 Cov.: 32 AF XY: 0.202 AC XY: 14986 AN XY: 74298

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.200

Alfa AF: 0.232 Hom.: 7323

Bravo AF: 0.197

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.3
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137111; hg19: chr15-77851535;