rs10489336

Variant names:

• chr1-209514837-G-A
• rs10489336

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 0.056 in 150,422 control chromosomes in the GnomAD database, including 502 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 0.056 (502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.0559 AC: 8407 AN: 150308 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0486

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

GnomAD4 genome AF: 0.0560 AC: 8418 AN: 150422 Hom.: 502 Cov.: 32 AF XY: 0.0555 AC XY: 4068 AN XY: 73330

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0481

Alfa AF: 0.0394 Hom.: 47

Bravo AF: 0.0609

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
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: rs10489336; hg19: chr1-209688182;