chr14-56304489-T-C

Variant names:

• chr14-56304489-T-C
• rs1152472
• ENST00000560296.2:n.392-820A>G

Variant summary

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

The ENST00000560296.2(ENSG00000259483):​n.392-820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,112 control chromosomes in the GnomAD database, including 22,323 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 0.54 (22323 hom., cov: 33)
• Consequence: ENSG00000259483 ENST00000560296.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.881
• Publications: 4 publications found

Genes affected

ENSG00000259483 (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 (SAS) allele frequency at 95% confidence interval = 0.617 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
ENSG00000259483	ENST00000560296.2	n.392-820A>G		intron_variant	Intron 3 of 3	4
ENSG00000259483	ENST00000732642.1	n.448-820A>G		intron_variant	Intron 3 of 3
ENSG00000259483	ENST00000732643.1	n.273-820A>G		intron_variant	Intron 2 of 2
ENSG00000259483	ENST00000732644.1	n.260-820A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81769 AN: 151992 Hom.: 22321 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.538 AC: 81806 AN: 152112 Hom.: 22323 Cov.: 33 AF XY: 0.541 AC XY: 40244 AN XY: 74354

African (AFR) AF: 0.436 AC: 18096 AN: 41508

American (AMR) AF: 0.566 AC: 8659 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3260 AN: 5160

South Asian (SAS) AF: 0.636 AC: 3065 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6052 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38915 AN: 67996

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.563 Hom.: 94012

Bravo AF: 0.534

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.45
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs1152472; hg19: chr14-56771207;