chr8-31295637-T-C

Variant names:

• chr8-31295637-T-C
• rs4634594
• ENST00000524022.1:n.213+19829T>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+19829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,758 control chromosomes in the GnomAD database, including 24,717 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 0.57 (24717 hom., cov: 30)
• Consequence: ENSG00000253377 ENST00000524022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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+19829T>C		intron	N/A
	ENSG00000253377	ENST00000655813.1		n.267+19829T>C		intron	N/A
	ENSG00000253377	ENST00000670110.2		n.242+19829T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86185 AN: 151644 Hom.: 24708 Cov.: 30

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.568 AC: 86236 AN: 151758 Hom.: 24717 Cov.: 30 AF XY: 0.569 AC XY: 42159 AN XY: 74138

African (AFR) AF: 0.561 AC: 23205 AN: 41334

American (AMR) AF: 0.574 AC: 8754 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4009 AN: 5118

South Asian (SAS) AF: 0.652 AC: 3137 AN: 4812

European-Finnish (FIN) AF: 0.516 AC: 5431 AN: 10534

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37760 AN: 67918

Other (OTH) AF: 0.570 AC: 1202 AN: 2110

Alfa AF: 0.563 Hom.: 12259

Bravo AF: 0.571

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.69
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4634594; hg19: chr8-31153153;