rs4904868

Variant names:

• chr14-92314657-T-C
• rs4904868
• ENST00000826664.1:n.259-584T>C

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.259-584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,142 control chromosomes in the GnomAD database, including 15,493 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 0.43 (15493 hom., cov: 33)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 12 publications found

Genes affected

ENSG00000307514 (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 (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370627	XR_944153.1	n.132-589T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307514	ENST00000826664.1	n.259-584T>C		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826665.1	n.254-589T>C		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826667.1	n.312-589T>C		intron_variant	Intron 2 of 2
ENSG00000307514	ENST00000826668.1	n.251-584T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64860 AN: 152024 Hom.: 15488 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.426 AC: 64883 AN: 152142 Hom.: 15493 Cov.: 33 AF XY: 0.423 AC XY: 31491 AN XY: 74368

African (AFR) AF: 0.225 AC: 9322 AN: 41516

American (AMR) AF: 0.368 AC: 5619 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1901 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4828

European-Finnish (FIN) AF: 0.541 AC: 5717 AN: 10570

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37446 AN: 67994

Other (OTH) AF: 0.415 AC: 877 AN: 2114

Alfa AF: 0.495 Hom.: 60726

Bravo AF: 0.399

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.71
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs4904868; hg19: chr14-92781001;