rs2474945

Variant names:

• chr1-118342291-A-C
• rs2474945

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 0.195 in 152,174 control chromosomes in the GnomAD database, including 3,032 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 0.19 (3032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.195 AC: 29590 AN: 152056 Hom.: 3030 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.195 AC: 29618 AN: 152174 Hom.: 3032 Cov.: 33 AF XY: 0.193 AC XY: 14335 AN XY: 74390

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0752

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.216

Alfa AF: 0.208 Hom.: 826

Bravo AF: 0.193

Asia WGS AF: 0.167 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2474945; hg19: chr1-118884914;