rs10506959

Variant names:

• chr12-88861946-C-T
• rs10506959

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 0.197 in 151,912 control chromosomes in the GnomAD database, including 3,662 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 0.20 (3662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.197 AC: 29872 AN: 151794 Hom.: 3648 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.197 AC: 29927 AN: 151912 Hom.: 3662 Cov.: 32 AF XY: 0.191 AC XY: 14206 AN XY: 74268

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.173

Alfa AF: 0.151 Hom.: 3783

Bravo AF: 0.211

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506959; hg19: chr12-89255723;