rs1454909

Variant names:

• chr5-57956571-C-T
• rs1454909
• ENST00000761558.1:n.149-18609C>T

Variant summary

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

The ENST00000761558.1(ENSG00000299201):​n.149-18609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,790 control chromosomes in the GnomAD database, including 19,926 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 0.49 (19926 hom., cov: 32)
• Consequence: ENSG00000299201 ENST00000761558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

Genes affected

ENSG00000299201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761558.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299201	ENST00000761558.1		n.149-18609C>T		intron	N/A
	ENSG00000299201	ENST00000761559.1		n.123-18609C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75146 AN: 151672 Hom.: 19942 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.495 AC: 75134 AN: 151790 Hom.: 19926 Cov.: 32 AF XY: 0.496 AC XY: 36824 AN XY: 74184

African (AFR) AF: 0.307 AC: 12706 AN: 41398

American (AMR) AF: 0.483 AC: 7363 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1943 AN: 5124

South Asian (SAS) AF: 0.612 AC: 2950 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6153 AN: 10550

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40108 AN: 67900

Other (OTH) AF: 0.513 AC: 1074 AN: 2094

Alfa AF: 0.565 Hom.: 13266

Bravo AF: 0.473

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.85
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1454909;

hg19: chr5-57252398;