rs1980421

Variant names:

• chr2-203745281-A-G
• rs1980421

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.826 AC: 34289 AN: 41520

American (AMR) AF: 0.817 AC: 12474 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4689 AN: 5188

South Asian (SAS) AF: 0.912 AC: 4395 AN: 4818

European-Finnish (FIN) AF: 0.817 AC: 8630 AN: 10568

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.758 AC: 51522 AN: 67958

Other (OTH) AF: 0.770 AC: 1624 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1980421; hg19: chr2-204610004;