5-88489807-C-T

Position:

• chr5-88489807-C-T

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, non coding transcript 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: ENST00000504034.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504034.2	n.25+8866G>A		intron_variant, non_coding_transcript_variant		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;