5-88489807-C-T

Variant names:

• chr5-88489807-C-T
• rs17478824
• ENST00000504034.2:n.25+8866G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504034.2(ENSG00000271904):​n.25+8866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,234 control chromosomes in the GnomAD database, including 555 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 0.082 (555 hom., cov: 32)
• Consequence: ENSG00000271904 ENST00000504034.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

ENSG00000271904 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0937 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
ENSG00000271904	ENST00000504034.2	n.25+8866G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12482 AN: 152116 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0956

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0820 AC: 12484 AN: 152234 Hom.: 555 Cov.: 32 AF XY: 0.0812 AC XY: 6045 AN XY: 74438

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0956

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0875 Hom.: 840

Bravo AF: 0.0779

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17478824; hg19: chr5-87785624;