2-137155725-A-G

Variant names:

• chr2-137155725-A-G
• rs882374
• NM_001316349.2:c.1370-4488A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001316349.2(THSD7B):​c.1370-4488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,092 control chromosomes in the GnomAD database, including 37,769 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 0.70 (37769 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.1370-4488A>G		intron_variant	Intron 5 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.947-4488A>G		intron_variant	Intron 5 of 27		XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.1370-4488A>G		intron_variant	Intron 5 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000485379.1	n.-235A>G		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106568 AN: 151974 Hom.: 37774 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.701 AC: 106587 AN: 152092 Hom.: 37769 Cov.: 32 AF XY: 0.699 AC XY: 51966 AN XY: 74358

African (AFR) AF: 0.624 AC: 25867 AN: 41458

American (AMR) AF: 0.689 AC: 10524 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2604 AN: 3468

East Asian (EAS) AF: 0.618 AC: 3197 AN: 5174

South Asian (SAS) AF: 0.576 AC: 2772 AN: 4814

European-Finnish (FIN) AF: 0.751 AC: 7959 AN: 10594

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51356 AN: 67990

Other (OTH) AF: 0.731 AC: 1542 AN: 2110

Alfa AF: 0.723 Hom.: 6043

Bravo AF: 0.691

Asia WGS AF: 0.601 AC: 2090 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.82
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs882374; hg19: chr2-137913295;