rs7736549

Variant names:

• chr5-80083715-C-A
• rs7736549
• ENST00000514042.1:n.-61G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000514042.1(THBS4-AS1):​n.-61G>T 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 ENST00000514042.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 9 publications found

Genes affected

THBS4-AS1 (HGNC:40583): (THBS4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
THBS4-AS1	NR_109930.1	n.-50G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THBS4-AS1	ENST00000514042.1	n.-61G>T		upstream_gene_variant		1
THBS4-AS1	ENST00000799170.1	n.-50G>T		upstream_gene_variant
THBS4-AS1	ENST00000799171.1	n.-51G>T		upstream_gene_variant

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.100 AC: 1 AN: 10

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.250 AC: 3 AN: 12

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0550 AC: 11 AN: 200

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.361 AC: 14984 AN: 41454

American (AMR) AF: 0.243 AC: 3718 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1518 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1174 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2199 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9494 AN: 68014

Other (OTH) AF: 0.231 AC: 487 AN: 2110

Alfa AF: 0.177 Hom.: 5517

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7736549; hg19: chr5-79379538;