2-137280927-T-C

Variant names:

• chr2-137280927-T-C
• rs10490733
• NM_001316349.2:c.2500+4901T>C

Variant summary

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

The NM_001316349.2(THSD7B):​c.2500+4901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,076 control chromosomes in the GnomAD database, including 2,562 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 0.17 (2562 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001316349.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	NM_001316349.2	MANE Select	c.2500+4901T>C		intron	N/A	NP_001303278.1	Q9C0I4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	ENST00000409968.6	TSL:5 MANE Select	c.2500+4901T>C		intron	N/A	ENSP00000387145.1	Q9C0I4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25201 AN: 151958 Hom.: 2554 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.166 AC: 25252 AN: 152076 Hom.: 2562 Cov.: 32 AF XY: 0.168 AC XY: 12493 AN XY: 74352

African (AFR) AF: 0.185 AC: 7675 AN: 41492

American (AMR) AF: 0.218 AC: 3325 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2499 AN: 5160

South Asian (SAS) AF: 0.123 AC: 595 AN: 4828

European-Finnish (FIN) AF: 0.108 AC: 1147 AN: 10602

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8394 AN: 67976

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.157 Hom.: 824

Bravo AF: 0.180

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		1.1
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: rs10490733; hg19: chr2-138038497;