chr12-88245913-C-T

Position:

• chr12-88245913-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 0.0228 in 152,146 control chromosomes in the GnomAD database, including 161 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 0.023 (161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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 (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0228 AC: 3460 AN: 152028 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0228 AC: 3465 AN: 152146 Hom.: 161 Cov.: 32 AF XY: 0.0242 AC XY: 1803 AN XY: 74366

Gnomad4 AFR AF: 0.00405

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.0233

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0147 Hom.: 47

Bravo AF: 0.0265

Asia WGS AF: 0.0800 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11104775; hg19: chr12-88639690;