rs283596

Variant names:

• chr5-73946886-A-G
• rs283596
• XR_001742745.1:n.789A>G

Variant summary

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

The XR_001742745.1(LOC105379034):​n.789A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,986 control chromosomes in the GnomAD database, including 12,788 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 0.41 (12788 hom., cov: 32)
• Consequence: LOC105379034 XR_001742745.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

Genes affected

LOC105379034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61953 AN: 151868 Hom.: 12776 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.408 AC: 61998 AN: 151986 Hom.: 12788 Cov.: 32 AF XY: 0.408 AC XY: 30317 AN XY: 74280

African (AFR) AF: 0.353 AC: 14640 AN: 41450

American (AMR) AF: 0.410 AC: 6258 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2211 AN: 5150

South Asian (SAS) AF: 0.494 AC: 2375 AN: 4810

European-Finnish (FIN) AF: 0.426 AC: 4502 AN: 10560

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29134 AN: 67956

Other (OTH) AF: 0.393 AC: 829 AN: 2112

Alfa AF: 0.431 Hom.: 7618

Bravo AF: 0.402

Asia WGS AF: 0.444 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.46
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs283596; hg19: chr5-73242711;