rs12150466

Variant names:

• chr17-44921166-C-T
• rs12150466
• ENST00000731540.1:n.114+362C>T

Variant summary

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

The ENST00000731540.1(ENSG00000295646):​n.114+362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 152,242 control chromosomes in the GnomAD database, including 267 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 0.051 (267 hom., cov: 32)
• Consequence: ENSG00000295646 ENST00000731540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 3 publications found

Genes affected

ENSG00000295646 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731540.1. 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
	ENSG00000295646	ENST00000731540.1		n.114+362C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7783 AN: 152124 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0511 AC: 7779 AN: 152242 Hom.: 267 Cov.: 32 AF XY: 0.0483 AC XY: 3592 AN XY: 74436

African (AFR) AF: 0.0250 AC: 1039 AN: 41550

American (AMR) AF: 0.0242 AC: 370 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5168

South Asian (SAS) AF: 0.0268 AC: 129 AN: 4820

European-Finnish (FIN) AF: 0.0505 AC: 536 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0794 AC: 5398 AN: 68006

Other (OTH) AF: 0.0374 AC: 79 AN: 2112

Alfa AF: 0.0685 Hom.: 228

Bravo AF: 0.0481

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.21
PhyloP100		-0.19

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: rs12150466;

hg19: chr17-42998534;