rs13405020

Positions:

• chr2-137384594-G-C
• chr2-137384594-G-T

Variant summary

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

The NM_001316349.2(THSD7B):​c.2501-21019G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,144 control chromosomes in the GnomAD database, including 3,399 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 0.20 (3399 hom., cov: 31)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7B	NM_001316349.2	c.2501-21019G>C		intron_variant		ENST00000409968.6
THSD7B	XM_047445935.1	c.2078-21019G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7B	ENST00000409968.6	c.2501-21019G>C		intron_variant		5	NM_001316349.2	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30284 AN: 152026 Hom.: 3397 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.199 AC: 30286 AN: 152144 Hom.: 3399 Cov.: 31 AF XY: 0.201 AC XY: 14943 AN XY: 74388

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.209

Alfa AF: 0.141 Hom.: 307

Bravo AF: 0.185

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.76

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: rs13405020; hg19: chr2-138142164;