chr5-91759840-C-T

Variant names:

• chr5-91759840-C-T
• rs6881283
• ENST00000651690.1:n.459-24017C>T

Variant summary

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

The ENST00000651690.1(ENSG00000286121):​n.459-24017C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,972 control chromosomes in the GnomAD database, including 3,743 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 0.20 (3743 hom., cov: 32)
• Consequence: ENSG00000286121 ENST00000651690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

ENSG00000286121 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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
ENSG00000286121	ENST00000651690.1	n.459-24017C>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31053 AN: 151854 Hom.: 3742 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.204 AC: 31048 AN: 151972 Hom.: 3743 Cov.: 32 AF XY: 0.208 AC XY: 15438 AN XY: 74258

Gnomad4 AFR AF: 0.0793

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.226

Alfa AF: 0.239 Hom.: 5733

Bravo AF: 0.199

Asia WGS AF: 0.248 AC: 858 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
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: rs6881283; hg19: chr5-91055657;