rs17786786

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024817.3(THSD4):​c.1015+59565A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,058 control chromosomes in the GnomAD database, including 8,151 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 0.32 ( 8151 hom., cov: 32)

Consequence

THSD4
NM_024817.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
THSD4NM_024817.3 linkuse as main transcriptc.1015+59565A>C intron_variant ENST00000261862.8 NP_079093.2 Q6ZMP0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
THSD4ENST00000261862.8 linkuse as main transcriptc.1015+59565A>C intron_variant 5 NM_024817.3 ENSP00000261862.8 Q6ZMP0-1
THSD4ENST00000355327.7 linkuse as main transcriptc.1015+59565A>C intron_variant 5 ENSP00000347484.3 Q6ZMP0-1

Frequencies

GnomAD3 genomes
AF:
0.325
AC:
49350
AN:
151940
Hom.:
8136
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.323
Gnomad AMI
AF:
0.342
Gnomad AMR
AF:
0.265
Gnomad ASJ
AF:
0.337
Gnomad EAS
AF:
0.267
Gnomad SAS
AF:
0.503
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.334
Gnomad OTH
AF:
0.342
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.325
AC:
49389
AN:
152058
Hom.:
8151
Cov.:
32
AF XY:
0.325
AC XY:
24187
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.337
Gnomad4 EAS
AF:
0.267
Gnomad4 SAS
AF:
0.503
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.334
Gnomad4 OTH
AF:
0.344
Alfa
AF:
0.337
Hom.:
5234
Bravo
AF:
0.319
Asia WGS
AF:
0.411
AC:
1433
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
3.1
DANN
Benign
0.30

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17786786; hg19: chr15-71608619; API