rs1254601

Variant names:

• chr14-52312827-G-A
• rs1254601
• ENST00000726803.1:n.1548C>T

Variant summary

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

The ENST00000726803.1(ENSG00000289424):​n.1548C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,016 control chromosomes in the GnomAD database, including 17,739 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 0.45 (17739 hom., cov: 31)
• Consequence: ENSG00000289424 ENST00000726803.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 3 publications found

Genes affected

ENSG00000289424 (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 = 0.603 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
ENSG00000289424	ENST00000726803.1	n.1548C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289424	ENST00000691625.3	n.435+9C>T		intron_variant	Intron 2 of 3
ENSG00000289424	ENST00000726797.1	n.299+9C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67888 AN: 151898 Hom.: 17748 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.446 AC: 67869 AN: 152016 Hom.: 17739 Cov.: 31 AF XY: 0.439 AC XY: 32617 AN XY: 74292

African (AFR) AF: 0.193 AC: 7988 AN: 41450

American (AMR) AF: 0.377 AC: 5767 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1558 AN: 5172

South Asian (SAS) AF: 0.317 AC: 1529 AN: 4816

European-Finnish (FIN) AF: 0.564 AC: 5948 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41334 AN: 67972

Other (OTH) AF: 0.470 AC: 991 AN: 2108

Alfa AF: 0.554 Hom.: 26963

Bravo AF: 0.423

Asia WGS AF: 0.311 AC: 1081 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	6.0
DANN	Benign	0.67
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1254601; hg19: chr14-52779545;