rs10489161

Variant names:

• chr1-25012308-G-A
• rs10489161

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 0.325 in 152,086 control chromosomes in the GnomAD database, including 10,114 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 0.33 (10114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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: 0.325 AC: 49355 AN: 151968 Hom.: 10082 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.325 AC: 49441 AN: 152086 Hom.: 10114 Cov.: 32 AF XY: 0.325 AC XY: 24146 AN XY: 74358

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.317

Alfa AF: 0.220 Hom.: 8532

Bravo AF: 0.350

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489161; hg19: chr1-25338799;