rs1424979

Variant names:

• chr2-53266504-A-T
• rs1424979

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 0.295 in 151,486 control chromosomes in the GnomAD database, including 6,874 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 0.30 (6874 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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: 0.295 AC: 44619 AN: 151374 Hom.: 6851 Cov.: 30

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.295 AC: 44693 AN: 151486 Hom.: 6874 Cov.: 30 AF XY: 0.295 AC XY: 21849 AN XY: 74044

African (AFR) AF: 0.330 AC: 13648 AN: 41338

American (AMR) AF: 0.198 AC: 3025 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3466

East Asian (EAS) AF: 0.166 AC: 858 AN: 5174

South Asian (SAS) AF: 0.412 AC: 1978 AN: 4800

European-Finnish (FIN) AF: 0.351 AC: 3618 AN: 10296

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19853 AN: 67866

Other (OTH) AF: 0.285 AC: 596 AN: 2094

Alfa AF: 0.302 Hom.: 886

Bravo AF: 0.278

Asia WGS AF: 0.285 AC: 980 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1424979; hg19: chr2-53493642;