rs10507029

Variant names:

• chr12-94143349-A-G
• rs10507029

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 0.0283 in 151,036 control chromosomes in the GnomAD database, including 115 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 0.028 (115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0597 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: 0.0283 AC: 4267 AN: 151008 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0588

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0285

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

GnomAD4 genome AF: 0.0283 AC: 4277 AN: 151036 Hom.: 115 Cov.: 32 AF XY: 0.0295 AC XY: 2176 AN XY: 73640

African (AFR) AF: 0.00569 AC: 234 AN: 41120

American (AMR) AF: 0.0624 AC: 948 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3470

East Asian (EAS) AF: 0.0270 AC: 139 AN: 5144

South Asian (SAS) AF: 0.0657 AC: 315 AN: 4794

European-Finnish (FIN) AF: 0.0390 AC: 396 AN: 10150

Middle Eastern (MID) AF: 0.0607 AC: 17 AN: 280

European-Non Finnish (NFE) AF: 0.0293 AC: 1988 AN: 67888

Other (OTH) AF: 0.0279 AC: 58 AN: 2082

Alfa AF: 0.0287 Hom.: 11

Bravo AF: 0.0270

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.016
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10507029; hg19: chr12-94537125;