rs10489789

Variant names:

• chr1-236516877-G-A
• rs10489789

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 0.16 in 152,184 control chromosomes in the GnomAD database, including 2,552 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 0.16 (2552 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.160 AC: 24331 AN: 152066 Hom.: 2535 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.160 AC: 24397 AN: 152184 Hom.: 2552 Cov.: 33 AF XY: 0.156 AC XY: 11621 AN XY: 74414

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0843

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.161

Alfa AF: 0.126 Hom.: 720

Bravo AF: 0.170

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489789; hg19: chr1-236680177;