rs2479393

Variant names:

• chr1-55022696-A-G
• rs2479393

Your query was ambiguous. Multiple possible variants found:

• chr1-55022696-A-G
• chr1-55022696-A-T

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 0.705 in 152,208 control chromosomes in the GnomAD database, including 38,177 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 0.71 (38177 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 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: 0.706 AC: 107301 AN: 152088 Hom.: 38171 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.705 AC: 107353 AN: 152208 Hom.: 38177 Cov.: 33 AF XY: 0.703 AC XY: 52324 AN XY: 74428

African (AFR) AF: 0.698 AC: 28971 AN: 41524

American (AMR) AF: 0.609 AC: 9307 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2485 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2486 AN: 5172

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4820

European-Finnish (FIN) AF: 0.777 AC: 8241 AN: 10612

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50295 AN: 68000

Other (OTH) AF: 0.676 AC: 1430 AN: 2114

Alfa AF: 0.702 Hom.: 16221

Bravo AF: 0.689

Asia WGS AF: 0.606 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.17
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2479393; hg19: chr1-55488369;