rs10489402

Variant names:

• chr1-186777424-C-A
• rs10489402

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 0.097 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.273 AC: 11335 AN: 41466

American (AMR) AF: 0.0551 AC: 842 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3472

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5178

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4824

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1854 AN: 68014

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0535 Hom.: 1666

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10489402; hg19: chr1-186746556;