rs113906

Positions:

• chr2-136901030-G-C
• chr2-136901030-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.139+18713G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,796 control chromosomes in the GnomAD database, including 15,733 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 0.43 (15733 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.139+18713G>C		intron_variant		ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-1206G>C		upstream_gene_variant			XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.139+18713G>C		intron_variant		5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.140-5418G>C		intron_variant		5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65678 AN: 151684 Hom.: 15741 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.433 AC: 65688 AN: 151796 Hom.: 15733 Cov.: 33 AF XY: 0.429 AC XY: 31817 AN XY: 74162

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.407

Alfa AF: 0.478 Hom.: 2199

Bravo AF: 0.408

Asia WGS AF: 0.204 AC: 712 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.40

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: rs113906; hg19: chr2-137658600;