rs2750097

Variant names:

• chr20-51112593-A-G
• rs2750097

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 0.338 in 152,084 control chromosomes in the GnomAD database, including 9,826 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 0.34 (9826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.338 AC: 51322 AN: 151966 Hom.: 9819 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.338 AC: 51331 AN: 152084 Hom.: 9826 Cov.: 32 AF XY: 0.343 AC XY: 25515 AN XY: 74344

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.345

Alfa AF: 0.364 Hom.: 2787

Bravo AF: 0.320

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2750097; hg19: chr20-49729130;