chr1-40119126-G-A

Variant names:

• chr1-40119126-G-A
• rs10493089

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 0.0926 in 151,890 control chromosomes in the GnomAD database, including 784 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 0.093 (784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14047 AN: 151772 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0926 AC: 14067 AN: 151890 Hom.: 784 Cov.: 32 AF XY: 0.0948 AC XY: 7038 AN XY: 74216

African (AFR) AF: 0.0679 AC: 2803 AN: 41298

American (AMR) AF: 0.142 AC: 2166 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0563 AC: 195 AN: 3466

East Asian (EAS) AF: 0.150 AC: 778 AN: 5178

South Asian (SAS) AF: 0.154 AC: 742 AN: 4812

European-Finnish (FIN) AF: 0.0956 AC: 1011 AN: 10570

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6104 AN: 67992

Other (OTH) AF: 0.0946 AC: 199 AN: 2104

Alfa AF: 0.0890 Hom.: 1214

Bravo AF: 0.0948

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10493089; hg19: chr1-40584798;