5-155476610-A-G

Variant names:

• chr5-155476610-A-G
• rs267015
• ENST00000758995.1:n.299-30473A>G

Variant summary

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

The ENST00000758995.1(ENSG00000298918):​n.299-30473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 151,764 control chromosomes in the GnomAD database, including 50,287 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 0.81 (50287 hom., cov: 31)
• Consequence: ENSG00000298918 ENST00000758995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 2 publications found

Genes affected

ENSG00000298918 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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
ENSG00000298918	ENST00000758995.1	n.299-30473A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123245 AN: 151646 Hom.: 50236 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.813 AC: 123357 AN: 151764 Hom.: 50287 Cov.: 31 AF XY: 0.816 AC XY: 60537 AN XY: 74154

African (AFR) AF: 0.797 AC: 33026 AN: 41434

American (AMR) AF: 0.849 AC: 12919 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2946 AN: 3460

East Asian (EAS) AF: 0.974 AC: 4995 AN: 5128

South Asian (SAS) AF: 0.890 AC: 4284 AN: 4816

European-Finnish (FIN) AF: 0.827 AC: 8739 AN: 10572

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53826 AN: 67832

Other (OTH) AF: 0.803 AC: 1687 AN: 2102

Alfa AF: 0.805 Hom.: 30870

Bravo AF: 0.811

Asia WGS AF: 0.914 AC: 3176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs267015; hg19: chr5-154856170;