rs12769316

Positions:

• chr10-102392994-G-A

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 0.131 in 152,084 control chromosomes in the GnomAD database, including 1,585 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 0.13 (1585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.131 AC: 19969 AN: 151966 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.131 AC: 19968 AN: 152084 Hom.: 1585 Cov.: 32 AF XY: 0.131 AC XY: 9745 AN XY: 74344

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0662

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.133

Alfa AF: 0.163 Hom.: 517

Bravo AF: 0.121

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12769316; hg19: chr10-104152751;