rs298158

chr1-60405454-G-Achr1-60405454-G-Cchr1-60405454-G-T

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 0.0488 in 152,130 control chromosomes in the GnomAD database, including 472 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 0.049 (472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7412 AN: 152012 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0187

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.000661

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0488 AC: 7418 AN: 152130 Hom.: 472 Cov.: 32 AF XY: 0.0504 AC XY: 3749 AN XY: 74366

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0187

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0475

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.000661

Gnomad4 NFE AF: 0.00387

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.000469 Hom.: 54

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs298158; hg19: chr1-60871126;