rs13015892

Positions:

• chr2-136852465-G-A
• chr2-136852465-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001316349.2(THSD7B):​c.-35-29679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,988 control chromosomes in the GnomAD database, including 2,737 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 (2737 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.802

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.-35-29679G>A		intron_variant		ENST00000409968.6	NP_001303278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.-35-29679G>A		intron_variant		5	NM_001316349.2	ENSP00000387145	P1
THSD7B	ENST00000472720.5	c.-35-29679G>A		intron_variant, NMD_transcript_variant		5		ENSP00000473349

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26259 AN: 151870 Hom.: 2742 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 26272 AN: 151988 Hom.: 2737 Cov.: 32 AF XY: 0.177 AC XY: 13128 AN XY: 74284

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.169

Alfa AF: 0.168 Hom.: 4040

Bravo AF: 0.182

Asia WGS AF: 0.328 AC: 1136 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.62

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: rs13015892; hg19: chr2-137610035;