rs8019546

Variant names:

• chr14-50857024-G-A
• rs8019546
• ENST00000557152.1:n.29-8490G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-50857024-G-A
• chr14-50857024-G-T

Variant summary

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

The ENST00000557152.1(ENSG00000258687):​n.29-8490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,012 control chromosomes in the GnomAD database, including 11,341 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 0.38 (11341 hom., cov: 31)
• Consequence: ENSG00000258687 ENST00000557152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 10 publications found

Genes affected

ENSG00000258687 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557152.1. 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
	ENSG00000258687	ENST00000557152.1	TSL:5	n.29-8490G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56917 AN: 151894 Hom.: 11310 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.375 AC: 57007 AN: 152012 Hom.: 11341 Cov.: 31 AF XY: 0.376 AC XY: 27911 AN XY: 74308

African (AFR) AF: 0.481 AC: 19950 AN: 41468

American (AMR) AF: 0.444 AC: 6766 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2718 AN: 5152

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2890 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20482 AN: 67984

Other (OTH) AF: 0.382 AC: 803 AN: 2104

Alfa AF: 0.337 Hom.: 19744

Bravo AF: 0.400

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.36
PhyloP100		-0.68

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: rs8019546;

hg19: chr14-51323742;