ENST00000519555.1:n.250+4906C>T

Variant names:

• chr8-6095422-G-A
• rs10503354
• ENST00000519555.1:n.250+4906C>T

Variant summary

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

The ENST00000519555.1(ENSG00000253880):​n.250+4906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,090 control chromosomes in the GnomAD database, including 2,392 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 0.18 (2392 hom., cov: 33)
• Consequence: ENSG00000253880 ENST00000519555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 3 publications found

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519555.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253880	ENST00000519555.1	TSL:4	n.250+4906C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26750 AN: 151972 Hom.: 2390 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.176 AC: 26767 AN: 152090 Hom.: 2392 Cov.: 33 AF XY: 0.180 AC XY: 13374 AN XY: 74344

African (AFR) AF: 0.198 AC: 8193 AN: 41472

American (AMR) AF: 0.209 AC: 3192 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1202 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4818

European-Finnish (FIN) AF: 0.200 AC: 2114 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10012 AN: 67976

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.157 Hom.: 8444

Bravo AF: 0.181

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs10503354; hg19: chr8-5952944;