rs10489216

Variant names:

• chr1-168633624-G-A
• rs10489216

Your query was ambiguous. Multiple possible variants found:

• chr1-168633624-G-A
• chr1-168633624-G-C

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 0.174 in 151,910 control chromosomes in the GnomAD database, including 2,761 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 0.17 (2761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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: 0.174 AC: 26414 AN: 151792 Hom.: 2764 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.174 AC: 26410 AN: 151910 Hom.: 2761 Cov.: 32 AF XY: 0.178 AC XY: 13197 AN XY: 74238

Gnomad4 AFR AF: 0.0618

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.225

Alfa AF: 0.207 Hom.: 3979

Bravo AF: 0.165

Asia WGS AF: 0.270 AC: 936 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
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: rs10489216; hg19: chr1-168602862;