chr5-73952687-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379034	XR_001742745.1	n.1400+5190A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304504	ENST00000803880.1	n.232+5190A>G		intron_variant	Intron 1 of 5
ENSG00000304504	ENST00000803884.1	n.148+5190A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs283610; hg19: chr5-73248512;