rs11952583

Variant names:

• chr5-74013280-A-C
• rs11952583
• ENST00000803880.1:n.704-28796A>C

Variant summary

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

The ENST00000803880.1(ENSG00000304504):​n.704-28796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 152,234 control chromosomes in the GnomAD database, including 54,361 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 0.84 (54361 hom., cov: 33)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619
• Publications: 2 publications found

Genes affected

ENSG00000304504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 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
ENSG00000304504	ENST00000803880.1	n.704-28796A>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127993 AN: 152116 Hom.: 54336 Cov.: 33

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.841 AC: 128065 AN: 152234 Hom.: 54361 Cov.: 33 AF XY: 0.842 AC XY: 62646 AN XY: 74430

African (AFR) AF: 0.736 AC: 30545 AN: 41516

American (AMR) AF: 0.807 AC: 12351 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3807 AN: 5166

South Asian (SAS) AF: 0.873 AC: 4203 AN: 4816

European-Finnish (FIN) AF: 0.909 AC: 9649 AN: 10620

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61704 AN: 68028

Other (OTH) AF: 0.847 AC: 1790 AN: 2114

Alfa AF: 0.863 Hom.: 81311

Bravo AF: 0.826

Asia WGS AF: 0.770 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs11952583; hg19: chr5-73309105;