rs1980421

Positions:

• chr2-203745281-A-G

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 0.794 in 152,110 control chromosomes in the GnomAD database, including 48,158 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 0.79 (48158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 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: 0.794 AC: 120751 AN: 151992 Hom.: 48112 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.794 AC: 120851 AN: 152110 Hom.: 48158 Cov.: 32 AF XY: 0.800 AC XY: 59485 AN XY: 74372

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.770

Alfa AF: 0.782 Hom.: 5786

Bravo AF: 0.794

Asia WGS AF: 0.891 AC: 3076 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1980421; hg19: chr2-204610004;