rs4982386

Variant names:

• chr14-20969149-T-C
• rs4982386
• ENST00000717680.1:n.346+8475A>G

Variant summary

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

The ENST00000717680.1(ENSG00000259130):​n.346+8475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,986 control chromosomes in the GnomAD database, including 11,668 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 0.38 (11668 hom., cov: 31)
• Consequence: ENSG00000259130 ENST00000717680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 5 publications found

Genes affected

ENSG00000259130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717680.1. 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
	ENSG00000259130	ENST00000717680.1		n.346+8475A>G		intron	N/A
	ENSG00000259130	ENST00000796665.1		n.772+2457A>G		intron	N/A
	ENSG00000259130	ENST00000796666.1		n.267+2457A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57486 AN: 151868 Hom.: 11667 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.378 AC: 57515 AN: 151986 Hom.: 11668 Cov.: 31 AF XY: 0.385 AC XY: 28620 AN XY: 74262

African (AFR) AF: 0.231 AC: 9581 AN: 41462

American (AMR) AF: 0.499 AC: 7631 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4808

European-Finnish (FIN) AF: 0.523 AC: 5513 AN: 10550

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28522 AN: 67954

Other (OTH) AF: 0.369 AC: 776 AN: 2104

Alfa AF: 0.384 Hom.: 4132

Bravo AF: 0.371

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs4982386; hg19: chr14-21437308;