ENST00000688936.3:n.123-61579G>A

Variant names:

• chr12-84122733-C-T
• rs1994104
• ENST00000688936.3:n.123-61579G>A

Variant summary

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

The ENST00000688936.3(ENSG00000289309):​n.123-61579G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 152,118 control chromosomes in the GnomAD database, including 711 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 0.083 (711 hom., cov: 32)
• Consequence: ENSG00000289309 ENST00000688936.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

ENSG00000289309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688936.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289309	ENST00000688936.3		n.123-61579G>A		intron	N/A
	ENSG00000289309	ENST00000689302.2		n.114-61579G>A		intron	N/A
	ENSG00000289309	ENST00000716306.1		n.112-61579G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12589 AN: 152000 Hom.: 710 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.0828 AC: 12593 AN: 152118 Hom.: 711 Cov.: 32 AF XY: 0.0777 AC XY: 5778 AN XY: 74390

African (AFR) AF: 0.155 AC: 6439 AN: 41488

American (AMR) AF: 0.0539 AC: 824 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.0124 AC: 60 AN: 4824

European-Finnish (FIN) AF: 0.0466 AC: 493 AN: 10586

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0636 AC: 4322 AN: 67996

Other (OTH) AF: 0.0764 AC: 161 AN: 2108

Alfa AF: 0.0785 Hom.: 799

Bravo AF: 0.0874

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1994104; hg19: chr12-84516512;