rs283596

Positions:

• chr5-73946886-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105379034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379034	XR_001742745.1	n.789A>G		non_coding_transcript_exon_variant	1/4
		n.73946886A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.393

Alfa AF: 0.431 Hom.: 6882

Bravo AF: 0.402

Asia WGS AF: 0.444 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283596; hg19: chr5-73242711;