NM_001316349.2:c.139+18713G>C

Variant names:

• chr2-136901030-G-C
• rs113906
• NM_001316349.2:c.139+18713G>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.139+18713G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,796 control chromosomes in the GnomAD database, including 15,733 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 0.43 (15733 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 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.139+18713G>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.139+18713G>C		intron	N/A	ENSP00000387145.1	Q9C0I4
	THSD7B	ENST00000472720.5	TSL:5	n.140-5418G>C		intron	N/A	ENSP00000473349.1	R4GMU2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65678 AN: 151684 Hom.: 15741 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.433 AC: 65688 AN: 151796 Hom.: 15733 Cov.: 33 AF XY: 0.429 AC XY: 31817 AN XY: 74162

African (AFR) AF: 0.270 AC: 11183 AN: 41356

American (AMR) AF: 0.373 AC: 5686 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1553 AN: 3472

East Asian (EAS) AF: 0.122 AC: 632 AN: 5162

South Asian (SAS) AF: 0.331 AC: 1589 AN: 4802

European-Finnish (FIN) AF: 0.566 AC: 5947 AN: 10504

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37513 AN: 67932

Other (OTH) AF: 0.407 AC: 858 AN: 2108

Alfa AF: 0.478 Hom.: 2199

Bravo AF: 0.408

Asia WGS AF: 0.204 AC: 712 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.18
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: rs113906; hg19: chr2-137658600;