chr5-159421063-T-C

Variant names:

• chr5-159421063-T-C
• rs4921496
• ENST00000635333.1:n.446-2960T>C

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.446-2960T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,176 control chromosomes in the GnomAD database, including 46,801 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 0.78 (46801 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -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 = 0.842 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.446-2960T>C		intron_variant	Intron 5 of 7	5
ENSG00000249738	ENST00000648969.1	n.172-2960T>C		intron_variant	Intron 2 of 2
ENSG00000249738	ENST00000636261.1	n.-151T>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119098 AN: 152058 Hom.: 46763 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.783 AC: 119188 AN: 152176 Hom.: 46801 Cov.: 32 AF XY: 0.790 AC XY: 58749 AN XY: 74410

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.814

Alfa AF: 0.767 Hom.: 88772

Bravo AF: 0.786

Asia WGS AF: 0.850 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4921496; hg19: chr5-158848071;