ENST00000554307.1:n.367-23523C>T

Variant names:

• chr14-79916682-G-A
• rs1534837
• ENST00000554307.1:n.367-23523C>T

Variant summary

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

The ENST00000554307.1(ENSG00000258416):​n.367-23523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,180 control chromosomes in the GnomAD database, including 348 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 0.060 (348 hom., cov: 32)
• Consequence: ENSG00000258416 ENST00000554307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 1 publications found

Genes affected

ENSG00000258416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554307.1. 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
	ENSG00000258416	ENST00000554307.1	TSL:3	n.367-23523C>T		intron	N/A
	ENSG00000258416	ENST00000836492.1		n.160+272C>T		intron	N/A
	ENSG00000258416	ENST00000836493.1		n.160+272C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9189 AN: 152060 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0604 AC: 9190 AN: 152180 Hom.: 348 Cov.: 32 AF XY: 0.0603 AC XY: 4487 AN XY: 74388

African (AFR) AF: 0.0268 AC: 1114 AN: 41532

American (AMR) AF: 0.0332 AC: 507 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3468

East Asian (EAS) AF: 0.119 AC: 616 AN: 5156

South Asian (SAS) AF: 0.123 AC: 593 AN: 4824

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10586

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0749 AC: 5091 AN: 68008

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0734 Hom.: 238

Bravo AF: 0.0546

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.2
DANN	Benign	0.76
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs1534837; hg19: chr14-80383025;