chr5-40490507-C-T

Variant names:

• chr5-40490507-C-T
• rs9283753
• ENST00000649444.1:n.242+4009C>T

Variant summary

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

The ENST00000649444.1(ENSG00000285552):​n.242+4009C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,012 control chromosomes in the GnomAD database, including 23,468 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 0.55 (23468 hom., cov: 32)
• Consequence: ENSG00000285552 ENST00000649444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

ENSG00000285552 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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
ENSG00000285552	ENST00000649444.1	n.242+4009C>T		intron_variant	Intron 2 of 2
ENSG00000285552	ENST00000649894.1	n.120-13364C>T		intron_variant	Intron 1 of 1
ENSG00000285616	ENST00000648975.1	n.-77G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83172 AN: 151894 Hom.: 23441 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.548 AC: 83239 AN: 152012 Hom.: 23468 Cov.: 32 AF XY: 0.537 AC XY: 39854 AN XY: 74276

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.527

Alfa AF: 0.562 Hom.: 3782

Bravo AF: 0.554

Asia WGS AF: 0.264 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9283753; hg19: chr5-40490609;