rs16838470

chr2-137254749-A-G

Variant summary

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

The NM_001316349.2(THSD7B):c.2266+12177A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,168 control chromosomes in the GnomAD database, including 109 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 0.027 (109 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7B	NM_001316349.2	c.2266+12177A>G		intron_variant		ENST00000409968.6
THSD7B	XM_047445935.1	c.1843+12177A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7B	ENST00000409968.6	c.2266+12177A>G		intron_variant		5	NM_001316349.2	P1

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4115 AN: 152050 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.00935

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0270 AC: 4109 AN: 152168 Hom.: 109 Cov.: 32 AF XY: 0.0281 AC XY: 2091 AN XY: 74394

Gnomad4 AFR AF: 0.0547

Gnomad4 AMR AF: 0.0207

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.0710

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00935

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0194 Hom.: 8

Bravo AF: 0.0285

Asia WGS AF: 0.0630 AC: 219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.4
Dann	Benign	0.76

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: rs16838470; hg19: chr2-138012319;