rs1254600

Variant names:

• chr14-52313735-A-G
• rs1254600
• ENST00000726798.1:n.332T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-52313735-A-G
• chr14-52313735-A-T

Variant summary

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

The ENST00000726798.1(ENSG00000289424):​n.332T>C 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 0.729 in 151,626 control chromosomes in the GnomAD database, including 41,755 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 0.73 (41755 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000726798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 22 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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 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	ENST00000726798.1	n.332T>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289424	ENST00000726800.1	n.376T>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289424	ENST00000726802.1	n.373T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110488 AN: 151506 Hom.: 41742 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.729 AC: 110533 AN: 151626 Hom.: 41755 Cov.: 32 AF XY: 0.719 AC XY: 53261 AN XY: 74118

African (AFR) AF: 0.572 AC: 23461 AN: 40990

American (AMR) AF: 0.660 AC: 10065 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2776 AN: 5156

South Asian (SAS) AF: 0.522 AC: 2520 AN: 4828

European-Finnish (FIN) AF: 0.786 AC: 8329 AN: 10592

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57818 AN: 68016

Other (OTH) AF: 0.752 AC: 1586 AN: 2110

Alfa AF: 0.818 Hom.: 80520

Bravo AF: 0.712

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs1254600; hg19: chr14-52780453;