rs6881283

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000286121 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651690.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286121	ENST00000651690.1		n.459-24017C>T		intron	N/A

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

African (AFR) AF: 0.0793 AC: 3290 AN: 41492

American (AMR) AF: 0.275 AC: 4201 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1436 AN: 5164

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4826

European-Finnish (FIN) AF: 0.287 AC: 3015 AN: 10516

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16633 AN: 67936

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.238 Hom.: 7320

Bravo AF: 0.199

Asia WGS AF: 0.248 AC: 858 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6881283;

hg19: chr5-91055657;