5-86878330-A-G

Variant names:

• chr5-86878330-A-G
• rs1493354
• ENST00000724121.1:n.149+45359T>C

Variant summary

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

The ENST00000724121.1(ENSG00000294529):​n.149+45359T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,038 control chromosomes in the GnomAD database, including 17,025 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 0.47 (17025 hom., cov: 32)
• Consequence: ENSG00000294529 ENST00000724121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 6 publications found

Genes affected

ENSG00000294529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724121.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294529	ENST00000724121.1		n.149+45359T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70846 AN: 151920 Hom.: 17021 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.466 AC: 70861 AN: 152038 Hom.: 17025 Cov.: 32 AF XY: 0.465 AC XY: 34573 AN XY: 74302

African (AFR) AF: 0.344 AC: 14291 AN: 41484

American (AMR) AF: 0.508 AC: 7763 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1714 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3336 AN: 5166

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4833 AN: 10544

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34418 AN: 67966

Other (OTH) AF: 0.487 AC: 1030 AN: 2114

Alfa AF: 0.496 Hom.: 32266

Bravo AF: 0.466

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1493354; hg19: chr5-86174147;