ENST00000725226.1:n.309+6931G>C

Variant names:

• chr12-4196806-C-G
• rs75615236
• ENST00000725226.1:n.309+6931G>C

Variant summary

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

The ENST00000725226.1(ENSG00000294684):​n.309+6931G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,216 control chromosomes in the GnomAD database, including 394 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 0.068 (394 hom., cov: 32)
• Consequence: ENSG00000294684 ENST00000725226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 3 publications found

Genes affected

ENSG00000294684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725226.1. 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
	ENSG00000294684	ENST00000725226.1		n.309+6931G>C		intron	N/A
	ENSG00000294684	ENST00000725227.1		n.243+6931G>C		intron	N/A
	ENSG00000294684	ENST00000725228.1		n.322+6843G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10343 AN: 152098 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0680 AC: 10344 AN: 152216 Hom.: 394 Cov.: 32 AF XY: 0.0670 AC XY: 4989 AN XY: 74428

African (AFR) AF: 0.0908 AC: 3770 AN: 41502

American (AMR) AF: 0.0725 AC: 1109 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5176

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4828

European-Finnish (FIN) AF: 0.0815 AC: 865 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0581 AC: 3951 AN: 68010

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0293 Hom.: 24

Bravo AF: 0.0691

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.72
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs75615236; hg19: chr12-4305972;