chr1-175837913-T-G

Variant names:

• chr1-175837913-T-G
• rs1750293

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 0.873 in 152,104 control chromosomes in the GnomAD database, including 58,210 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 0.87 (58210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.873 AC: 132747 AN: 151986 Hom.: 58165 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.873 AC: 132845 AN: 152104 Hom.: 58210 Cov.: 31 AF XY: 0.872 AC XY: 64844 AN XY: 74336

African (AFR) AF: 0.936 AC: 38856 AN: 41522

American (AMR) AF: 0.835 AC: 12753 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3086 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4868 AN: 5170

South Asian (SAS) AF: 0.841 AC: 4041 AN: 4806

European-Finnish (FIN) AF: 0.814 AC: 8582 AN: 10540

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57708 AN: 68000

Other (OTH) AF: 0.884 AC: 1867 AN: 2112

Alfa AF: 0.860 Hom.: 6992

Bravo AF: 0.874

Asia WGS AF: 0.878 AC: 3050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1750293; hg19: chr1-175807049;