rs2195830

Positions:

• chr2-137085943-C-G
• chr2-137085943-C-T

Variant summary

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

The NM_001316349.2(THSD7B):​c.951-8930C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,074 control chromosomes in the GnomAD database, including 13,768 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 0.39 (13768 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.951-8930C>G		intron_variant		ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.528-8930C>G		intron_variant			XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.951-8930C>G		intron_variant		5	NM_001316349.2	ENSP00000387145	P1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59324 AN: 151956 Hom.: 13723 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.391 AC: 59434 AN: 152074 Hom.: 13768 Cov.: 33 AF XY: 0.385 AC XY: 28624 AN XY: 74332

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.372

Alfa AF: 0.328 Hom.: 1132

Bravo AF: 0.422

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
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: rs2195830; hg19: chr2-137843513;