ENST00000524132.6:n.530-25008T>C

Variant names:

• chr8-36562484-A-G
• rs10503991
• ENST00000524132.6:n.530-25008T>C

Variant summary

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

The ENST00000524132.6(ENSG00000253363):​n.530-25008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,102 control chromosomes in the GnomAD database, including 4,596 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 0.20 (4596 hom., cov: 32)
• Consequence: ENSG00000253363 ENST00000524132.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 5 publications found

Genes affected

ENSG00000253363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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
ENSG00000253363	ENST00000524132.6	n.530-25008T>C		intron_variant	Intron 4 of 4	4
ENSG00000253363	ENST00000651399.1	n.517-66772T>C		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2	n.485-135420T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30745 AN: 151984 Hom.: 4579 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.203 AC: 30808 AN: 152102 Hom.: 4596 Cov.: 32 AF XY: 0.204 AC XY: 15137 AN XY: 74358

African (AFR) AF: 0.415 AC: 17208 AN: 41446

American (AMR) AF: 0.139 AC: 2116 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1394 AN: 5162

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4812

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6835 AN: 68010

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.111 Hom.: 726

Bravo AF: 0.211

Asia WGS AF: 0.305 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.81
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10503991; hg19: chr8-36420002;