ENST00000753113.1:n.126-659A>G

Variant names:

• chr12-4224753-T-C
• rs11611647
• ENST00000753113.1:n.126-659A>G

Variant summary

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

The ENST00000753113.1(ENSG00000298123):​n.126-659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,204 control chromosomes in the GnomAD database, including 3,811 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 0.22 (3811 hom., cov: 32)
• Consequence: ENSG00000298123 ENST00000753113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 21 publications found

Genes affected

ENSG00000298123 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753113.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298123	ENST00000753113.1		n.126-659A>G		intron	N/A
	ENSG00000298123	ENST00000753114.1		n.169-1159A>G		intron	N/A
	ENSG00000298123	ENST00000753115.1		n.166-1159A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33516 AN: 152086 Hom.: 3805 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.221 AC: 33562 AN: 152204 Hom.: 3811 Cov.: 32 AF XY: 0.222 AC XY: 16522 AN XY: 74420

African (AFR) AF: 0.240 AC: 9983 AN: 41522

American (AMR) AF: 0.224 AC: 3419 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1205 AN: 5184

South Asian (SAS) AF: 0.149 AC: 716 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2393 AN: 10594

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14346 AN: 68002

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.215 Hom.: 12233

Bravo AF: 0.223

Asia WGS AF: 0.195 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.57
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs11611647; hg19: chr12-4333919;