5-108626024-T-A

Variant names:

• chr5-108626024-T-A
• rs6594324
• ENST00000718521.1:n.174-2709A>T

Variant summary

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

The ENST00000718521.1(ENSG00000293711):​n.174-2709A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,152 control chromosomes in the GnomAD database, including 40,318 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 0.73 (40318 hom., cov: 33)
• Consequence: ENSG00000293711 ENST00000718521.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 2 publications found

Genes affected

ENSG00000293711 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718521.1. 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
	ENSG00000293711	ENST00000718521.1		n.174-2709A>T		intron	N/A
	ENSG00000293711	ENST00000718522.1		n.175-10358A>T		intron	N/A
	ENSG00000293711	ENST00000718523.1		n.280-2709A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110523 AN: 152034 Hom.: 40310 Cov.: 33

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.727 AC: 110571 AN: 152152 Hom.: 40318 Cov.: 33 AF XY: 0.722 AC XY: 53723 AN XY: 74370

African (AFR) AF: 0.769 AC: 31919 AN: 41526

American (AMR) AF: 0.655 AC: 10006 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2748 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3540 AN: 5176

South Asian (SAS) AF: 0.615 AC: 2969 AN: 4824

European-Finnish (FIN) AF: 0.720 AC: 7614 AN: 10574

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49318 AN: 67998

Other (OTH) AF: 0.721 AC: 1522 AN: 2110

Alfa AF: 0.610 Hom.: 1643

Bravo AF: 0.728

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6594324; hg19: chr5-107961725; COSMIC: COSV60181004;