14-39627781-A-G

Variant names:

• chr14-39627781-A-G
• rs744511
• ENST00000650911.1:n.113-27723A>G

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.113-27723A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,020 control chromosomes in the GnomAD database, including 14,528 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 0.42 (14528 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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.113-27723A>G		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.641-14932A>G		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.153-27723A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63232 AN: 151902 Hom.: 14512 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.416 AC: 63299 AN: 152020 Hom.: 14528 Cov.: 32 AF XY: 0.418 AC XY: 31090 AN XY: 74318

African (AFR) AF: 0.613 AC: 25409 AN: 41464

American (AMR) AF: 0.350 AC: 5340 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2336 AN: 5160

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4824

European-Finnish (FIN) AF: 0.386 AC: 4079 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21917 AN: 67966

Other (OTH) AF: 0.365 AC: 768 AN: 2102

Alfa AF: 0.347 Hom.: 42009

Bravo AF: 0.416

Asia WGS AF: 0.510 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.73
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs744511; hg19: chr14-40096985;