rs1002007

Variant names:

• chr15-71289711-G-A
• rs1002007
• NM_024817.3:c.1015+32996G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-71289711-G-A
• chr15-71289711-G-C
• chr15-71289711-G-T

Variant summary

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

The NM_024817.3(THSD4):​c.1015+32996G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,070 control chromosomes in the GnomAD database, including 4,821 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 0.24 (4821 hom., cov: 32)
• Consequence: THSD4 NM_024817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

Genes affected

THSD4 (HGNC:25835): (thrombospondin type 1 domain containing 4) Predicted to enable hydrolase activity. Predicted to be an extracellular matrix structural constituent. Predicted to act upstream of or within elastic fiber assembly. Located in collagen-containing extracellular matrix and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

THSD4 Gene-Disease associations (from GenCC):

• aortic aneurysm, familial thoracic 12

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Franklin by Genoox

LOC124903521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD4	NM_024817.3	c.1015+32996G>A		intron_variant	Intron 6 of 17	ENST00000261862.8	NP_079093.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD4	ENST00000261862.8	c.1015+32996G>A		intron_variant	Intron 6 of 17	5	NM_024817.3	ENSP00000261862.8

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36558 AN: 151952 Hom.: 4820 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.241 AC: 36573 AN: 152070 Hom.: 4821 Cov.: 32 AF XY: 0.240 AC XY: 17859 AN XY: 74336

African (AFR) AF: 0.204 AC: 8463 AN: 41472

American (AMR) AF: 0.229 AC: 3508 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2899 AN: 5148

South Asian (SAS) AF: 0.153 AC: 739 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10576

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16394 AN: 67982

Other (OTH) AF: 0.201 AC: 425 AN: 2114

Alfa AF: 0.233 Hom.: 3589

Bravo AF: 0.237

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1002007; hg19: chr15-71582050;