8-73757555-G-T

Variant names:

• chr8-73757555-G-T
• rs6980645
• ENST00000358757.5:n.443-17687C>A

Variant summary

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

The ENST00000358757.5(ENSG00000258677):​n.443-17687C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 151,046 control chromosomes in the GnomAD database, including 59,978 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 0.89 (59978 hom., cov: 26)
• Consequence: ENSG00000258677 ENST00000358757.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

ENSG00000258677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
ENSG00000258677	ENST00000358757.5	n.443-17687C>A		intron_variant	Intron 5 of 7	4		ENSP00000454445.2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 134345 AN: 150928 Hom.: 59941 Cov.: 26

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.890 AC: 134436 AN: 151046 Hom.: 59978 Cov.: 26 AF XY: 0.888 AC XY: 65489 AN XY: 73732

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.916

Alfa AF: 0.895 Hom.: 55171

Bravo AF: 0.889

Asia WGS AF: 0.907 AC: 3153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6980645; hg19: chr8-74669790;