chr12-67985701-C-T

Position:

• chr12-67985701-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 0.745 in 152,014 control chromosomes in the GnomAD database, including 42,354 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 0.75 (42354 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 0.745 AC: 113200 AN: 151896 Hom.: 42325 Cov.: 30

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.745 AC: 113282 AN: 152014 Hom.: 42354 Cov.: 30 AF XY: 0.747 AC XY: 55511 AN XY: 74296

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.767

Alfa AF: 0.762 Hom.: 7537

Bravo AF: 0.752

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2906852; hg19: chr12-68379481;