rs2479418

Variant names:

• chr1-55029204-A-G
• rs2479418

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 0.421 in 152,008 control chromosomes in the GnomAD database, including 14,035 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 0.42 (14035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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: 0.421 AC: 63987 AN: 151890 Hom.: 14024 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.421 AC: 64020 AN: 152008 Hom.: 14035 Cov.: 31 AF XY: 0.419 AC XY: 31142 AN XY: 74290

African (AFR) AF: 0.342 AC: 14161 AN: 41440

American (AMR) AF: 0.411 AC: 6280 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5168

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4822

European-Finnish (FIN) AF: 0.491 AC: 5182 AN: 10550

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32307 AN: 67974

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.456 Hom.: 8411

Bravo AF: 0.406

Asia WGS AF: 0.327 AC: 1136 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	1.0
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2479418; hg19: chr1-55494877;