5-159399302-G-C

Variant names:

• chr5-159399302-G-C
• rs918520
• ENST00000635333.1:n.327+6725G>C

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+6725G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,220 control chromosomes in the GnomAD database, including 51,474 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 0.82 (51474 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000249738	ENST00000635333.1	n.327+6725G>C		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-17222G>C		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-17222G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124903 AN: 152102 Hom.: 51444 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.821 AC: 124984 AN: 152220 Hom.: 51474 Cov.: 32 AF XY: 0.826 AC XY: 61441 AN XY: 74420

African (AFR) AF: 0.796 AC: 33038 AN: 41520

American (AMR) AF: 0.871 AC: 13326 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2924 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5172 AN: 5184

South Asian (SAS) AF: 0.879 AC: 4236 AN: 4820

European-Finnish (FIN) AF: 0.837 AC: 8872 AN: 10596

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54628 AN: 68014

Other (OTH) AF: 0.842 AC: 1778 AN: 2112

Alfa AF: 0.770 Hom.: 2422

Bravo AF: 0.824

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.88
DANN	Benign	0.62
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs918520; hg19: chr5-158826310;