2-137118305-T-C

Position:

• chr2-137118305-T-C

Variant summary

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

The NM_001316349.2(THSD7B):​c.1369+3012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,026 control chromosomes in the GnomAD database, including 20,815 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 0.50 (20815 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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 = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.1369+3012T>C		intron_variant		ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.946+3012T>C		intron_variant			XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.1369+3012T>C		intron_variant		5	NM_001316349.2	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76221 AN: 151908 Hom.: 20822 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.501 AC: 76233 AN: 152026 Hom.: 20815 Cov.: 32 AF XY: 0.506 AC XY: 37625 AN XY: 74318

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.481

Alfa AF: 0.566 Hom.: 34304

Bravo AF: 0.475

Asia WGS AF: 0.440 AC: 1532 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.64

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: rs1469622; hg19: chr2-137875875;