12-96876545-G-T

Position:

• chr12-96876545-G-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 0.586 in 152,016 control chromosomes in the GnomAD database, including 26,843 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 0.59 (26843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.586 AC: 88963 AN: 151898 Hom.: 26797 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.586 AC: 89069 AN: 152016 Hom.: 26843 Cov.: 32 AF XY: 0.580 AC XY: 43071 AN XY: 74262

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.562

Alfa AF: 0.537 Hom.: 9199

Bravo AF: 0.603

Asia WGS AF: 0.638 AC: 2219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs185198; hg19: chr12-97270323;