ENST00000524085.2:n.299-8472G>A

Variant names:

• chr8-81489445-G-A
• rs16909233
• ENST00000524085.2:n.299-8472G>A

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-8472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,098 control chromosomes in the GnomAD database, including 1,336 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 0.12 (1336 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 9 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+27471G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-8472G>A		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-32262G>A		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-32262G>A		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-32262G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18832 AN: 151980 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.124 AC: 18841 AN: 152098 Hom.: 1336 Cov.: 32 AF XY: 0.121 AC XY: 9026 AN XY: 74358

African (AFR) AF: 0.0768 AC: 3187 AN: 41496

American (AMR) AF: 0.0970 AC: 1482 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.145 AC: 698 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1233 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11291 AN: 67962

Other (OTH) AF: 0.122 AC: 258 AN: 2108

Alfa AF: 0.142 Hom.: 297

Bravo AF: 0.117

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.26
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs16909233; hg19: chr8-82401680;