rs10047589

Variant names:

• chr12-104350610-C-T
• rs10047589

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 0.326 in 152,166 control chromosomes in the GnomAD database, including 8,261 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 (8261 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49501 AN: 152048 Hom.: 8252 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.326 AC: 49540 AN: 152166 Hom.: 8261 Cov.: 33 AF XY: 0.328 AC XY: 24430 AN XY: 74388

African (AFR) AF: 0.365 AC: 15138 AN: 41478

American (AMR) AF: 0.253 AC: 3877 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1106 AN: 5182

South Asian (SAS) AF: 0.301 AC: 1449 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4396 AN: 10588

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21367 AN: 68010

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.318 Hom.: 982

Bravo AF: 0.314

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10047589; hg19: chr12-104744388;