12-40383514-T-G

Variant names:

• chr12-40383514-T-G
• rs12423567
• ENST00000724141.1:n.307+32787A>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+32787A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,118 control chromosomes in the GnomAD database, including 6,342 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 0.28 (6342 hom., cov: 32)
• Consequence: ENSG00000258167 ENST00000724141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 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

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
	ENSG00000258167	ENST00000724141.1		n.307+32787A>C		intron	N/A
	ENSG00000258167	ENST00000724142.1		n.170-34735A>C		intron	N/A
	ENSG00000258167	ENST00000724143.1		n.170-34735A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42461 AN: 152000 Hom.: 6335 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.279 AC: 42493 AN: 152118 Hom.: 6342 Cov.: 32 AF XY: 0.280 AC XY: 20826 AN XY: 74362

African (AFR) AF: 0.187 AC: 7760 AN: 41484

American (AMR) AF: 0.285 AC: 4360 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 994 AN: 3472

East Asian (EAS) AF: 0.134 AC: 693 AN: 5174

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3927 AN: 10582

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22379 AN: 67984

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.188 Hom.: 425

Bravo AF: 0.270

Asia WGS AF: 0.183 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.25
PhyloP100		-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12423567;

hg19: chr12-40777316;