rs10047589

chr12-104350610-C-T

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 0.326 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.306

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10047589; hg19: chr12-104744388;