rs958413

Variant names:

• chr1-218112832-G-C
• rs958413

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 0.116 in 152,188 control chromosomes in the GnomAD database, including 1,254 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 0.12 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.116 AC: 17659 AN: 152070 Hom.: 1250 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.116 AC: 17673 AN: 152188 Hom.: 1254 Cov.: 32 AF XY: 0.119 AC XY: 8834 AN XY: 74392

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0446

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.112

Alfa AF: 0.138 Hom.: 195

Bravo AF: 0.107

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958413; hg19: chr1-218286174;