5-159405269-C-A

Variant names:

• chr5-159405269-C-A
• rs4921492
• ENST00000635333.1:n.328-11255C>A

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.328-11255C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,922 control chromosomes in the GnomAD database, including 8,382 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 0.33 (8382 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 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.328-11255C>A		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-11255C>A		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-11255C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50484 AN: 151802 Hom.: 8365 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.333 AC: 50537 AN: 151922 Hom.: 8382 Cov.: 31 AF XY: 0.330 AC XY: 24513 AN XY: 74224

African (AFR) AF: 0.316 AC: 13091 AN: 41416

American (AMR) AF: 0.293 AC: 4464 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 827 AN: 3464

East Asian (EAS) AF: 0.376 AC: 1933 AN: 5144

South Asian (SAS) AF: 0.361 AC: 1736 AN: 4804

European-Finnish (FIN) AF: 0.319 AC: 3369 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23962 AN: 67956

Other (OTH) AF: 0.349 AC: 736 AN: 2106

Alfa AF: 0.301 Hom.: 2528

Bravo AF: 0.331

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4921492; hg19: chr5-158832277;