chr12-9751478-C-A

Position:

• chr12-9751478-C-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 0.252 in 151,876 control chromosomes in the GnomAD database, including 5,003 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 0.25 (5003 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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 = 0.264 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: 0.252 AC: 38213 AN: 151756 Hom.: 5002 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.252 AC: 38253 AN: 151876 Hom.: 5003 Cov.: 31 AF XY: 0.249 AC XY: 18497 AN XY: 74232

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.239

Alfa AF: 0.159 Hom.: 332

Bravo AF: 0.252

Asia WGS AF: 0.125 AC: 436 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	5.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3176806; hg19: chr12-9904074;