rs282381

Variant names:

• chr5-73981548-G-A
• rs282381
• ENST00000803880.1:n.430-817G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-73981548-G-A
• chr5-73981548-G-C

Variant summary

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

The ENST00000803880.1(ENSG00000304504):​n.430-817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,140 control chromosomes in the GnomAD database, including 28,475 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 0.60 (28475 hom., cov: 33)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379034	XR_001742745.1	n.1598-817G>A		intron_variant	Intron 3 of 3
LOC105379034	XR_001742746.1	n.340-817G>A		intron_variant	Intron 2 of 2
LOC105379034	XR_007058819.1	n.262-817G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304504	ENST00000803880.1	n.430-817G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91681 AN: 152022 Hom.: 28416 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.603 AC: 91802 AN: 152140 Hom.: 28475 Cov.: 33 AF XY: 0.606 AC XY: 45085 AN XY: 74370

African (AFR) AF: 0.691 AC: 28685 AN: 41504

American (AMR) AF: 0.665 AC: 10175 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4623 AN: 5184

South Asian (SAS) AF: 0.669 AC: 3228 AN: 4824

European-Finnish (FIN) AF: 0.543 AC: 5731 AN: 10558

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35789 AN: 67986

Other (OTH) AF: 0.573 AC: 1212 AN: 2114

Alfa AF: 0.544 Hom.: 37402

Bravo AF: 0.613

Asia WGS AF: 0.748 AC: 2599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.48
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs282381; hg19: chr5-73277373;