rs10489402

Variant names:

• chr1-186777424-C-A
• rs10489402

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 0.097 in 152,166 control chromosomes in the GnomAD database, including 1,655 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 0.097 (1655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.0967 AC: 14709 AN: 152048 Hom.: 1636 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0970 AC: 14766 AN: 152166 Hom.: 1655 Cov.: 32 AF XY: 0.0947 AC XY: 7049 AN XY: 74402

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0804

Alfa AF: 0.0352 Hom.: 369

Bravo AF: 0.108

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489402; hg19: chr1-186746556;