2-136797654-T-C

Variant names:

• chr2-136797654-T-C
• rs1427593
• NM_001316349.2:c.-36+31967T>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.-36+31967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,780 control chromosomes in the GnomAD database, including 39,614 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 0.72 (39614 hom., cov: 31)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 17 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.-36+31967T>C		intron_variant	Intron 1 of 27	ENST00000409968.6	NP_001303278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.-36+31967T>C		intron_variant	Intron 1 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.-36+31967T>C		intron_variant	Intron 1 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109072 AN: 151662 Hom.: 39587 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.719 AC: 109157 AN: 151780 Hom.: 39614 Cov.: 31 AF XY: 0.723 AC XY: 53630 AN XY: 74196

African (AFR) AF: 0.759 AC: 31404 AN: 41388

American (AMR) AF: 0.686 AC: 10449 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2239 AN: 3468

East Asian (EAS) AF: 0.974 AC: 5013 AN: 5146

South Asian (SAS) AF: 0.819 AC: 3943 AN: 4816

European-Finnish (FIN) AF: 0.736 AC: 7776 AN: 10570

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46076 AN: 67858

Other (OTH) AF: 0.686 AC: 1445 AN: 2106

Alfa AF: 0.694 Hom.: 136961

Bravo AF: 0.716

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		-0.73
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: rs1427593; hg19: chr2-137555224;