ENST00000653824.3:n.507T>C

Variant names:

• chr1-166339048-T-C
• rs7543540
• ENST00000653824.3:n.507T>C

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.507T>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 0.461 in 151,968 control chromosomes in the GnomAD database, including 18,541 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 0.46 (18541 hom., cov: 32)
• Consequence: ENSG00000229588 ENST00000653824.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 2 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653824.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229588	ENST00000653824.3		n.507T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000229588	ENST00000829274.1		n.327T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69954 AN: 151850 Hom.: 18500 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.461 AC: 70059 AN: 151968 Hom.: 18541 Cov.: 32 AF XY: 0.464 AC XY: 34501 AN XY: 74288

African (AFR) AF: 0.713 AC: 29576 AN: 41466

American (AMR) AF: 0.472 AC: 7212 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3626 AN: 5154

South Asian (SAS) AF: 0.440 AC: 2114 AN: 4810

European-Finnish (FIN) AF: 0.336 AC: 3550 AN: 10554

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21658 AN: 67916

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.409 Hom.: 2472

Bravo AF: 0.487

Asia WGS AF: 0.572 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs7543540; hg19: chr1-166308285;