5-159399485-A-G

Variant names:

• chr5-159399485-A-G
• rs918518
• ENST00000635333.1:n.327+6908A>G

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+6908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,188 control chromosomes in the GnomAD database, including 50,713 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 (50713 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 7 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635333.1. 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
	ENSG00000249738	ENST00000635333.1	TSL:5	n.327+6908A>G		intron	N/A
	ENSG00000249738	ENST00000641150.1		n.533-17039A>G		intron	N/A
	ENSG00000249738	ENST00000648969.1		n.54-17039A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123920 AN: 152070 Hom.: 50666 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.815 AC: 124020 AN: 152188 Hom.: 50713 Cov.: 32 AF XY: 0.821 AC XY: 61044 AN XY: 74398

African (AFR) AF: 0.817 AC: 33934 AN: 41518

American (AMR) AF: 0.861 AC: 13159 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2964 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5180

South Asian (SAS) AF: 0.899 AC: 4329 AN: 4818

European-Finnish (FIN) AF: 0.821 AC: 8711 AN: 10604

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52989 AN: 67988

Other (OTH) AF: 0.838 AC: 1774 AN: 2116

Alfa AF: 0.808 Hom.: 7835

Bravo AF: 0.819

Asia WGS AF: 0.937 AC: 3257 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	3.8
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs918518; hg19: chr5-158826493;