rs12359499

Positions:

• chr10-128622414-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 0.196 in 151,990 control chromosomes in the GnomAD database, including 3,076 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 (3076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.196 AC: 29787 AN: 151874 Hom.: 3075 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.196 AC: 29808 AN: 151990 Hom.: 3076 Cov.: 31 AF XY: 0.192 AC XY: 14272 AN XY: 74266

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.179

Alfa AF: 0.187 Hom.: 2588

Bravo AF: 0.199

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.028
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12359499; hg19: chr10-130420678;