rs10489532

Variant names:

• chr1-115192428-C-T
• rs10489532

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.258 in 152,108 control chromosomes in the GnomAD database, including 6,453 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 0.26 (6453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.258 AC: 39287 AN: 151990 Hom.: 6454 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.258 AC: 39270 AN: 152108 Hom.: 6453 Cov.: 32 AF XY: 0.251 AC XY: 18684 AN XY: 74358

African (AFR) AF: 0.0874 AC: 3628 AN: 41526

American (AMR) AF: 0.226 AC: 3457 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3472

East Asian (EAS) AF: 0.00310 AC: 16 AN: 5160

South Asian (SAS) AF: 0.166 AC: 800 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3689 AN: 10554

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25214 AN: 67978

Other (OTH) AF: 0.290 AC: 612 AN: 2110

Alfa AF: 0.302 Hom.: 1355

Bravo AF: 0.244

Asia WGS AF: 0.0880 AC: 309 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	0.086
DANN	Benign	0.58
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10489532; hg19: chr1-115735049;