15-71282460-G-C

Position:

• chr15-71282460-G-C

Variant summary

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

The NM_024817.3(THSD4):​c.1015+25745G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 144,962 control chromosomes in the GnomAD database, including 29,465 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 0.64 (29465 hom., cov: 31)
• Consequence: THSD4 NM_024817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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]

LOC124903521 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD4	NM_024817.3	c.1015+25745G>C		intron_variant		ENST00000261862.8
LOC124903521	XR_007064701.1	n.6337G>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD4	ENST00000261862.8	c.1015+25745G>C		intron_variant		5	NM_024817.3	P1
THSD4	ENST00000355327.7	c.1015+25745G>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 93293 AN: 144836 Hom.: 29455 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.644 AC: 93333 AN: 144962 Hom.: 29465 Cov.: 31 AF XY: 0.645 AC XY: 45496 AN XY: 70590

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.650

Alfa AF: 0.544 Hom.: 1670

Bravo AF: 0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs9806183; hg19: chr15-71574799;