rs1021639

Positions:

• chr1-214230538-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 0.778 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;