5-3092078-C-T

Variant names:

• chr5-3092078-C-T
• rs6873793
• ENST00000733078.1:n.496+88G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000733078.1(ENSG00000295848):​n.496+88G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,042 control chromosomes in the GnomAD database, including 24,437 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 0.56 (24437 hom., cov: 33)
• Consequence: ENSG00000295848 ENST00000733078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 7 publications found

Genes affected

ENSG00000295848 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733078.1. 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
	ENSG00000295848	ENST00000733078.1		n.496+88G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84737 AN: 151924 Hom.: 24401 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.558 AC: 84834 AN: 152042 Hom.: 24437 Cov.: 33 AF XY: 0.549 AC XY: 40829 AN XY: 74308

African (AFR) AF: 0.644 AC: 26691 AN: 41472

American (AMR) AF: 0.573 AC: 8766 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2149 AN: 3468

East Asian (EAS) AF: 0.182 AC: 938 AN: 5160

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4818

European-Finnish (FIN) AF: 0.469 AC: 4954 AN: 10570

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37473 AN: 67946

Other (OTH) AF: 0.568 AC: 1200 AN: 2114

Alfa AF: 0.554 Hom.: 87930

Bravo AF: 0.569

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		0.12

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: rs6873793;

hg19: chr5-3092192;