chr14-54116469-T-C

Variant names:

• chr14-54116469-T-C
• rs728425
• ENST00000747857.1:n.595-24372A>G

Variant summary

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

The ENST00000747857.1(ENSG00000297427):​n.595-24372A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,044 control chromosomes in the GnomAD database, including 25,635 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 0.55 (25635 hom., cov: 32)
• Consequence: ENSG00000297427 ENST00000747857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 3 publications found

Genes affected

ENSG00000297427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370507	XR_943882.3	n.665-24372A>G		intron_variant	Intron 4 of 6
LOC105370507	XR_943883.3	n.664+67558A>G		intron_variant	Intron 4 of 5
LOC105370507	XR_943884.2	n.665-6449A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297427	ENST00000747857.1	n.595-24372A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83622 AN: 151926 Hom.: 25636 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.550 AC: 83631 AN: 152044 Hom.: 25635 Cov.: 32 AF XY: 0.556 AC XY: 41299 AN XY: 74328

African (AFR) AF: 0.259 AC: 10730 AN: 41494

American (AMR) AF: 0.558 AC: 8509 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2482 AN: 5158

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4818

European-Finnish (FIN) AF: 0.750 AC: 7943 AN: 10596

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46493 AN: 67958

Other (OTH) AF: 0.572 AC: 1208 AN: 2112

Alfa AF: 0.647 Hom.: 15324

Bravo AF: 0.519

Asia WGS AF: 0.572 AC: 1988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs728425; hg19: chr14-54583187;