rs9283753

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

Genes affected

ENSG00000285552 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649444.1. 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
	ENSG00000285552	ENST00000649444.1		n.242+4009C>T		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.120-13364C>T		intron	N/A
	ENSG00000285616	ENST00000648975.1		n.-77G>A		upstream_gene	N/A

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

African (AFR) AF: 0.587 AC: 24337 AN: 41494

American (AMR) AF: 0.506 AC: 7730 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3464

East Asian (EAS) AF: 0.191 AC: 988 AN: 5172

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4822

European-Finnish (FIN) AF: 0.494 AC: 5209 AN: 10540

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39743 AN: 67938

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9283753; hg19: chr5-40490609;