rs10850408

Positions:

• chr12-114942588-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 0.312 in 152,036 control chromosomes in the GnomAD database, including 7,703 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 0.31 (7703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47334 AN: 151920 Hom.: 7694 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.312 AC: 47372 AN: 152036 Hom.: 7703 Cov.: 32 AF XY: 0.307 AC XY: 22821 AN XY: 74320

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.329

Alfa AF: 0.329 Hom.: 11245

Bravo AF: 0.313

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10850408; hg19: chr12-115380393;