8-5292591-C-T

Variant names:

• chr8-5292591-C-T
• rs1420838
• ENST00000778535.1:n.43-3730G>A

Variant summary

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

The ENST00000778535.1(ENSG00000301371):​n.43-3730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 151,996 control chromosomes in the GnomAD database, including 49,767 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 0.79 (49767 hom., cov: 30)
• Consequence: ENSG00000301371 ENST00000778535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

Genes affected

ENSG00000301371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778535.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301371	ENST00000778535.1		n.43-3730G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119729 AN: 151880 Hom.: 49756 Cov.: 30

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.788 AC: 119778 AN: 151996 Hom.: 49767 Cov.: 30 AF XY: 0.791 AC XY: 58806 AN XY: 74310

African (AFR) AF: 0.499 AC: 20667 AN: 41408

American (AMR) AF: 0.897 AC: 13680 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3662 AN: 5164

South Asian (SAS) AF: 0.873 AC: 4209 AN: 4824

European-Finnish (FIN) AF: 0.903 AC: 9544 AN: 10574

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62152 AN: 67984

Other (OTH) AF: 0.828 AC: 1748 AN: 2110

Alfa AF: 0.878 Hom.: 243467

Bravo AF: 0.773

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.50
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1420838; hg19: chr8-5150113;