rs10493089

Positions:

• chr1-40119126-G-A
• chr1-40119126-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 0.0926 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40119126G>A		intergenic_region

Ensembl

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

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0878 Hom.: 953

Bravo AF: 0.0948

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493089; hg19: chr1-40584798;