rs10489216

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;