rs4444253

Variant names:

• chr14-25107780-C-T
• rs4444253
• ENST00000790916.1:n.386-13845G>A

Variant summary

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

The ENST00000790916.1(ENSG00000302997):​n.386-13845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,168 control chromosomes in the GnomAD database, including 1,015 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 0.11 (1015 hom., cov: 32)
• Consequence: ENSG00000302997 ENST00000790916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 0 publications found

Genes affected

ENSG00000302997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302997	ENST00000790916.1	n.386-13845G>A		intron_variant	Intron 2 of 2
ENSG00000302997	ENST00000790917.1	n.89+4992G>A		intron_variant	Intron 1 of 1
ENSG00000302997	ENST00000790918.1	n.89+4992G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16669 AN: 152050 Hom.: 1016 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.110 AC: 16678 AN: 152168 Hom.: 1015 Cov.: 32 AF XY: 0.109 AC XY: 8114 AN XY: 74366

African (AFR) AF: 0.0605 AC: 2514 AN: 41526

American (AMR) AF: 0.111 AC: 1702 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.121 AC: 583 AN: 4810

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10582

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9627 AN: 67998

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.117 Hom.: 184

Bravo AF: 0.105

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4444253; hg19: chr14-25576986;