2-137118305-T-C

Variant names:

• chr2-137118305-T-C
• rs1469622
• NM_001316349.2:c.1369+3012T>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.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
• Publications: 7 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=-0.87).
• 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 rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.1369+3012T>C		intron_variant	Intron 5 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.946+3012T>C		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.1369+3012T>C		intron_variant	Intron 5 of 27	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

African (AFR) AF: 0.294 AC: 12188 AN: 41462

American (AMR) AF: 0.491 AC: 7499 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1565 AN: 3466

East Asian (EAS) AF: 0.540 AC: 2796 AN: 5176

South Asian (SAS) AF: 0.408 AC: 1965 AN: 4822

European-Finnish (FIN) AF: 0.746 AC: 7894 AN: 10576

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40557 AN: 67950

Other (OTH) AF: 0.481 AC: 1013 AN: 2106

Alfa AF: 0.555 Hom.: 53655

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
PhyloP100		0.17
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: rs1469622; hg19: chr2-137875875;