rs2868088

Variant names:

• chr20-44285012-A-G
• rs2868088

Your query was ambiguous. Multiple possible variants found:

• chr20-44285012-A-G
• chr20-44285012-A-T

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 0.32 in 151,898 control chromosomes in the GnomAD database, including 8,608 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 0.32 (8608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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 (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.319 AC: 48439 AN: 151780 Hom.: 8572 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.320 AC: 48533 AN: 151898 Hom.: 8608 Cov.: 32 AF XY: 0.327 AC XY: 24261 AN XY: 74240

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.341

Alfa AF: 0.300 Hom.: 1458

Bravo AF: 0.338

Asia WGS AF: 0.467 AC: 1623 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	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868088; hg19: chr20-42913652;