rs10496768

Positions:

• chr2-137322384-G-A

Variant summary

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

The NM_001316349.2(THSD7B):​c.2500+46358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,222 control chromosomes in the GnomAD database, including 889 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 0.095 (889 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7B	NM_001316349.2	c.2500+46358G>A		intron_variant		ENST00000409968.6
THSD7B	XM_047445935.1	c.2077+46358G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7B	ENST00000409968.6	c.2500+46358G>A		intron_variant		5	NM_001316349.2	P1

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14410 AN: 152102 Hom.: 888 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0946 AC: 14406 AN: 152222 Hom.: 889 Cov.: 32 AF XY: 0.0941 AC XY: 7003 AN XY: 74432

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0531

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.111

Alfa AF: 0.121 Hom.: 589

Bravo AF: 0.0895

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.52

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: rs10496768; hg19: chr2-138079954;