12-119251654-A-G

Variant names:

• chr12-119251654-A-G
• rs4576883
• ENST00000536009.1:n.69+7295T>C

Variant summary

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

The ENST00000536009.1(ENSG00000256311):​n.69+7295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,220 control chromosomes in the GnomAD database, including 1,668 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 0.14 (1668 hom., cov: 33)
• Consequence: ENSG00000256311 ENST00000536009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 2 publications found

Genes affected

ENSG00000256311 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536009.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256311	ENST00000536009.1	TSL:3	n.69+7295T>C		intron	N/A
	ENSG00000256311	ENST00000847923.1		n.162+7295T>C		intron	N/A
	ENSG00000256311	ENST00000847924.1		n.440-1148T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21669 AN: 152100 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.143 AC: 21696 AN: 152220 Hom.: 1668 Cov.: 33 AF XY: 0.141 AC XY: 10507 AN XY: 74416

African (AFR) AF: 0.191 AC: 7935 AN: 41524

American (AMR) AF: 0.109 AC: 1660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3470

East Asian (EAS) AF: 0.0767 AC: 397 AN: 5176

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1169 AN: 10608

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8275 AN: 68016

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.129 Hom.: 1561

Bravo AF: 0.140

Asia WGS AF: 0.194 AC: 676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.70
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4576883; hg19: chr12-119689459;