8-2804298-G-C

Variant names:

• chr8-2804298-G-C
• rs1454973
• ENST00000520024.1:n.177-288G>C

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.177-288G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 152,204 control chromosomes in the GnomAD database, including 23 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 0.012 (23 hom., cov: 33)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 1 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. 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
	LOC105377785	NR_168441.1		n.539-288G>C		intron	N/A
	LOC105377785	NR_168442.1		n.539-288G>C		intron	N/A
	LOC105377785	NR_168443.1		n.539-288G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.177-288G>C		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.532-288G>C		intron	N/A
	ENSG00000253853	ENST00000662575.1		n.82-288G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1879 AN: 152088 Hom.: 21 Cov.: 33

Gnomad AFR AF: 0.00374

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00793

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.00576

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0124 AC: 1886 AN: 152204 Hom.: 23 Cov.: 33 AF XY: 0.0126 AC XY: 938 AN XY: 74402

African (AFR) AF: 0.00373 AC: 155 AN: 41526

American (AMR) AF: 0.00792 AC: 121 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.0657 AC: 340 AN: 5178

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4822

European-Finnish (FIN) AF: 0.00576 AC: 61 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 932 AN: 68006

Other (OTH) AF: 0.0156 AC: 33 AN: 2112

Alfa AF: 0.0104 Hom.: 2

Bravo AF: 0.0122

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1454973; hg19: chr8-2661816;