5-155127535-A-G

Variant names:

• chr5-155127535-A-G
• rs6882113
• ENST00000660390.1:n.281+39825A>G

Variant summary

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

The ENST00000660390.1(ENSG00000287963):​n.281+39825A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,196 control chromosomes in the GnomAD database, including 4,019 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 0.22 (4019 hom., cov: 33)
• Consequence: ENSG00000287963 ENST00000660390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

Genes affected

ENSG00000287963 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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
ENSG00000287963	ENST00000660390.1	n.281+39825A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32900 AN: 152078 Hom.: 4002 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00866

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.217 AC: 32955 AN: 152196 Hom.: 4019 Cov.: 33 AF XY: 0.214 AC XY: 15919 AN XY: 74428

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.193

Alfa AF: 0.203 Hom.: 788

Bravo AF: 0.214

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6882113; hg19: chr5-154507095;