rs7736549

Positions:

• chr5-80083715-C-A
• chr5-80083715-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 5-80083715-C-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,380 control chromosomes in the GnomAD database, including 4,597 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 0.23 (4595 hom., cov: 33)
  • Exomes 𝑓: 0.061 (2 hom.)
• Consequence: THBS4-AS1 NR_109930.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

THBS4-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THBS4-AS1	NR_109930.1			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34390 AN: 152018 Hom.: 4585 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.0615 AC: 15 AN: 244 Hom.: 2 AF XY: 0.0797 AC XY: 11 AN XY: 138

Gnomad4 AMR exome AF: 0.100

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0550

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.226 AC: 34438 AN: 152136 Hom.: 4595 Cov.: 33 AF XY: 0.230 AC XY: 17136 AN XY: 74390

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.231

Alfa AF: 0.158 Hom.: 757

Bravo AF: 0.237

Asia WGS AF: 0.316 AC: 1097 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7736549; hg19: chr5-79379538;