rs1534837

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370582	XR_944054.3	n.189+272C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258416	ENST00000554307.1	n.367-23523C>T		intron_variant	Intron 2 of 2	3
ENSG00000258416	ENST00000836492.1	n.160+272C>T		intron_variant	Intron 1 of 1
ENSG00000258416	ENST00000836493.1	n.160+272C>T		intron_variant	Intron 1 of 1

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 v4.3

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;