5-73952687-A-G

Variant names:

• chr5-73952687-A-G
• rs283610
• ENST00000803880.1:n.232+5190A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000803880.1(ENSG00000304504):​n.232+5190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,092 control chromosomes in the GnomAD database, including 13,460 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 0.42 (13460 hom., cov: 33)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 9 publications found

Genes affected

ENSG00000304504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803880.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304504	ENST00000803880.1		n.232+5190A>G		intron	N/A
	ENSG00000304504	ENST00000803884.1		n.148+5190A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63821 AN: 151974 Hom.: 13441 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.420 AC: 63878 AN: 152092 Hom.: 13460 Cov.: 33 AF XY: 0.420 AC XY: 31206 AN XY: 74376

African (AFR) AF: 0.406 AC: 16824 AN: 41476

American (AMR) AF: 0.414 AC: 6337 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2224 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4457 AN: 10546

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28807 AN: 67998

Other (OTH) AF: 0.395 AC: 835 AN: 2112

Alfa AF: 0.422 Hom.: 51714

Bravo AF: 0.416

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs283610;

hg19: chr5-73248512;