5-91759840-C-T

Position:

• chr5-91759840-C-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, non coding transcript 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: ENST00000651690.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651690.1	n.459-24017C>T		intron_variant, non_coding_transcript_variant

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;