rs10506698

chr12-74651637-T-C

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 0.078 in 152,286 control chromosomes in the GnomAD database, including 605 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 0.078 (605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0779 AC: 11858 AN: 152168 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0780 AC: 11871 AN: 152286 Hom.: 605 Cov.: 32 AF XY: 0.0766 AC XY: 5702 AN XY: 74462

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.0210

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0962 Hom.: 134

Bravo AF: 0.0704

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506698; hg19: chr12-75045417;