8-31317314-T-C

Variant names:

• chr8-31317314-T-C
• rs2575029
• ENST00000524022.1:n.213+41506T>C

Variant summary

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

The ENST00000524022.1(ENSG00000253377):​n.213+41506T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,136 control chromosomes in the GnomAD database, including 53,112 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 0.83 (53112 hom., cov: 31)
• Consequence: ENSG00000253377 ENST00000524022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 4 publications found

Genes affected

ENSG00000253377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524022.1. 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
	ENSG00000253377	ENST00000524022.1	TSL:3	n.213+41506T>C		intron	N/A
	ENSG00000253377	ENST00000655813.1		n.267+41506T>C		intron	N/A
	ENSG00000253377	ENST00000670110.2		n.243-4563T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126870 AN: 152018 Hom.: 53068 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.835 AC: 126969 AN: 152136 Hom.: 53112 Cov.: 31 AF XY: 0.833 AC XY: 61936 AN XY: 74364

African (AFR) AF: 0.827 AC: 34306 AN: 41490

American (AMR) AF: 0.824 AC: 12586 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3116 AN: 3468

East Asian (EAS) AF: 0.921 AC: 4760 AN: 5168

South Asian (SAS) AF: 0.839 AC: 4047 AN: 4824

European-Finnish (FIN) AF: 0.804 AC: 8528 AN: 10604

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56876 AN: 67996

Other (OTH) AF: 0.854 AC: 1806 AN: 2114

Alfa AF: 0.837 Hom.: 133580

Bravo AF: 0.836

Asia WGS AF: 0.884 AC: 3074 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2575029; hg19: chr8-31174830;