ENST00000519555.1:n.250+4254C>A

Variant names:

• chr8-6096074-G-T
• rs10503355
• ENST00000519555.1:n.250+4254C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519555.1(ENSG00000253880):​n.250+4254C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,186 control chromosomes in the GnomAD database, including 538 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 0.063 (538 hom., cov: 32)
• Consequence: ENSG00000253880 ENST00000519555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253880	ENST00000519555.1	n.250+4254C>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9486 AN: 152068 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00788

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0625 AC: 9517 AN: 152186 Hom.: 538 Cov.: 32 AF XY: 0.0610 AC XY: 4539 AN XY: 74420

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0297

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00810

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0278 Hom.: 115

Bravo AF: 0.0663

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503355; hg19: chr8-5953596;