12-6734681-A-G

Position:

• chr12-6734681-A-G

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 0.718 in 151,904 control chromosomes in the GnomAD database, including 39,272 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 0.72 (39272 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6734681A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108924 AN: 151786 Hom.: 39242 Cov.: 30

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109001 AN: 151904 Hom.: 39272 Cov.: 30 AF XY: 0.721 AC XY: 53532 AN XY: 74236

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.715

Alfa AF: 0.693 Hom.: 22085

Bravo AF: 0.720

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2365567; hg19: chr12-6843847;