rs1748363

Variant names:

• chr1-158189930-C-T
• rs1748363

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0184 AC: 764 AN: 41498

American (AMR) AF: 0.0922 AC: 1409 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3468

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5186

South Asian (SAS) AF: 0.0839 AC: 404 AN: 4814

European-Finnish (FIN) AF: 0.108 AC: 1140 AN: 10566

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7451 AN: 67972

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.0816 Hom.: 306

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
PhyloP100		-0.41

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;