14-39535687-A-G

Variant names:

• chr14-39535687-A-G
• rs12431815
• ENST00000650911.1:n.112+65287A>G

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.112+65287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,202 control chromosomes in the GnomAD database, including 1,010 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 0.10 (1010 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 3 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650911.1. 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
	ENSG00000258526	ENST00000650911.1		n.112+65287A>G		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.566+2834A>G		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.152+65287A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15698 AN: 152084 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.103 AC: 15693 AN: 152202 Hom.: 1010 Cov.: 32 AF XY: 0.101 AC XY: 7504 AN XY: 74404

African (AFR) AF: 0.0411 AC: 1708 AN: 41540

American (AMR) AF: 0.0879 AC: 1344 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3468

East Asian (EAS) AF: 0.0734 AC: 381 AN: 5188

South Asian (SAS) AF: 0.118 AC: 567 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10568

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9629 AN: 68010

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.127 Hom.: 4178

Bravo AF: 0.0975

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.025
DANN	Benign	0.31
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs12431815; hg19: chr14-40004891;