ENST00000724141.1:n.307+44174T>C

Variant names:

• chr12-40372127-A-G
• rs7962370
• ENST00000724141.1:n.307+44174T>C

Variant summary

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

The ENST00000724141.1(ENSG00000258167):​n.307+44174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 151,992 control chromosomes in the GnomAD database, including 56,494 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 0.86 (56494 hom., cov: 32)
• Consequence: ENSG00000258167 ENST00000724141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 3 publications found

Genes affected

ENSG00000258167 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724141.1. 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
	ENSG00000258167	ENST00000724141.1		n.307+44174T>C		intron	N/A
	ENSG00000258167	ENST00000724142.1		n.170-23348T>C		intron	N/A
	ENSG00000258167	ENST00000724143.1		n.170-23348T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130881 AN: 151874 Hom.: 56450 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.862 AC: 130981 AN: 151992 Hom.: 56494 Cov.: 32 AF XY: 0.863 AC XY: 64095 AN XY: 74276

African (AFR) AF: 0.836 AC: 34685 AN: 41508

American (AMR) AF: 0.883 AC: 13438 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3090 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3540 AN: 5162

South Asian (SAS) AF: 0.864 AC: 4163 AN: 4818

European-Finnish (FIN) AF: 0.904 AC: 9578 AN: 10592

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59548 AN: 67916

Other (OTH) AF: 0.872 AC: 1840 AN: 2110

Alfa AF: 0.871 Hom.: 9025

Bravo AF: 0.857

Asia WGS AF: 0.761 AC: 2647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.43
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7962370; hg19: chr12-40765929;