rs10506959

chr12-88861946-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 0.197 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;