rs1748363

chr1-158189930-C-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 0.0794 in 152,100 control chromosomes in the GnomAD database, including 626 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 0.079 (626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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 (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0796 AC: 12091 AN: 151982 Hom.: 626 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0849

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0794 AC: 12079 AN: 152100 Hom.: 626 Cov.: 32 AF XY: 0.0798 AC XY: 5932 AN XY: 74344

Gnomad4 AFR AF: 0.0184

Gnomad4 AMR AF: 0.0922

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.0946 Hom.: 225

Bravo AF: 0.0746

Asia WGS AF: 0.0550 AC: 191 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	3.3
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1748363; hg19: chr1-158159720;