rs2479417

Variant names:

• chr1-55030071-T-C
• rs2479417

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 0.542 in 151,712 control chromosomes in the GnomAD database, including 23,550 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 0.54 (23550 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.32
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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: 0.542 AC: 82194 AN: 151594 Hom.: 23541 Cov.: 29

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.542 AC: 82226 AN: 151712 Hom.: 23550 Cov.: 29 AF XY: 0.536 AC XY: 39759 AN XY: 74142

African (AFR) AF: 0.392 AC: 16216 AN: 41326

American (AMR) AF: 0.509 AC: 7761 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1697 AN: 5136

South Asian (SAS) AF: 0.398 AC: 1901 AN: 4772

European-Finnish (FIN) AF: 0.647 AC: 6823 AN: 10542

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43927 AN: 67914

Other (OTH) AF: 0.540 AC: 1137 AN: 2106

Alfa AF: 0.598 Hom.: 35996

Bravo AF: 0.525

Asia WGS AF: 0.372 AC: 1293 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	0.20
DANN	Benign	0.40
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs2479417; hg19: chr1-55495744;