rs2479418

Positions:

• chr1-55029204-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.402

Alfa AF: 0.457 Hom.: 7544

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2479418; hg19: chr1-55494877;