rs1021639

Variant names:

• chr1-214230538-G-A
• rs1021639

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 0.778 in 151,972 control chromosomes in the GnomAD database, including 46,134 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 0.78 (46134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 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: 0.779 AC: 118229 AN: 151856 Hom.: 46105 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.778 AC: 118306 AN: 151972 Hom.: 46134 Cov.: 31 AF XY: 0.778 AC XY: 57817 AN XY: 74290

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.797

Alfa AF: 0.795 Hom.: 9646

Bravo AF: 0.779

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021639; hg19: chr1-214403881;