12-91626998-T-C

Variant names:

• chr12-91626998-T-C
• rs7133883
• ENST00000685093.1:n.503+6727A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685093.1(ENSG00000289605):​n.503+6727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,152 control chromosomes in the GnomAD database, including 40,347 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 0.71 (40347 hom., cov: 32)
• Consequence: ENSG00000289605 ENST00000685093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 1 publications found

Genes affected

ENSG00000289605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685093.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289605	ENST00000685093.1		n.503+6727A>G		intron	N/A
	ENSG00000289605	ENST00000834583.1		n.515+6727A>G		intron	N/A
	ENSG00000289605	ENST00000834584.1		n.227+6727A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108038 AN: 152034 Hom.: 40281 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.711 AC: 108168 AN: 152152 Hom.: 40347 Cov.: 32 AF XY: 0.710 AC XY: 52776 AN XY: 74370

African (AFR) AF: 0.926 AC: 38439 AN: 41516

American (AMR) AF: 0.734 AC: 11223 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4939 AN: 5180

South Asian (SAS) AF: 0.675 AC: 3254 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6169 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.593 AC: 40294 AN: 67980

Other (OTH) AF: 0.677 AC: 1427 AN: 2108

Alfa AF: 0.504 Hom.: 1317

Bravo AF: 0.736

Asia WGS AF: 0.839 AC: 2916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.41
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7133883; hg19: chr12-92020775;