2-136797654-T-C

Position:

• chr2-136797654-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
THSD7B	NM_001316349.2	c.-36+31967T>C		intron_variant		ENST00000409968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7B	ENST00000409968.6	c.-36+31967T>C		intron_variant		5	NM_001316349.2	P1
THSD7B	ENST00000472720.5	c.-36+31967T>C		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.686

Alfa AF: 0.693 Hom.: 58655

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

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: rs1427593; hg19: chr2-137555224;