rs10490741

chr2-137119394-G-A

Variant summary

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

The NM_001316349.2(THSD7B):c.1369+4101G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,230 control chromosomes in the GnomAD database, including 228 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 0.051 (228 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

THSD7B (HGNC:29348): (thrombospondin type 1 domain containing 7B) Predicted to be involved in actin cytoskeleton reorganization. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7B	NM_001316349.2	c.1369+4101G>A		intron_variant		ENST00000409968.6
THSD7B	XM_047445935.1	c.946+4101G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7B	ENST00000409968.6	c.1369+4101G>A		intron_variant		5	NM_001316349.2	P1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7716 AN: 152112 Hom.: 228 Cov.: 33

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0508 AC: 7726 AN: 152230 Hom.: 228 Cov.: 33 AF XY: 0.0521 AC XY: 3874 AN XY: 74424

Gnomad4 AFR AF: 0.0761

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.0912

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0308

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0382 Hom.: 57

Bravo AF: 0.0508

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.8
Dann	Benign	0.52

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: rs10490741; hg19: chr2-137876964;