rs10506989

Variant names:

• chr12-90493093-G-A
• rs10506989

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 0.271 in 151,790 control chromosomes in the GnomAD database, including 6,901 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 0.27 (6901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.271 AC: 41115 AN: 151670 Hom.: 6886 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 151790 Hom.: 6901 Cov.: 32 AF XY: 0.271 AC XY: 20068 AN XY: 74180

African (AFR) AF: 0.472 AC: 19539 AN: 41360

American (AMR) AF: 0.259 AC: 3963 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5166

South Asian (SAS) AF: 0.297 AC: 1428 AN: 4814

European-Finnish (FIN) AF: 0.177 AC: 1862 AN: 10512

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 11997 AN: 67884

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.209 Hom.: 861

Bravo AF: 0.283

Asia WGS AF: 0.343 AC: 1182 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.40
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10506989; hg19: chr12-90886870;