rs2474945

Positions:

• chr1-118342291-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;