rs538928

Variant names:

• chr2-21166147-A-G
• rs538928

Your query was ambiguous. Multiple possible variants found:

• chr2-21166147-A-G
• chr2-21166147-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 0.766 in 150,288 control chromosomes in the GnomAD database, including 44,585 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 0.77 (44585 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.766 AC: 114995 AN: 150190 Hom.: 44550 Cov.: 29

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.808

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.766 AC: 115077 AN: 150288 Hom.: 44585 Cov.: 29 AF XY: 0.767 AC XY: 56279 AN XY: 73338

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.762

Alfa AF: 0.725 Hom.: 2729

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3180 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.022
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538928; hg19: chr2-21389019;