rs12618360

Variant names:

• chr2-137255503-G-A
• rs12618360
• NM_001316349.2:c.2266+12931G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001316349.2(THSD7B):​c.2266+12931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,160 control chromosomes in the GnomAD database, including 108 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 (108 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.2266+12931G>A		intron_variant	Intron 10 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.1843+12931G>A		intron_variant	Intron 10 of 27		XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.2266+12931G>A		intron_variant	Intron 10 of 27	5	NM_001316349.2	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4106 AN: 152042 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0111

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: 0.0269 AC: 4100 AN: 152160 Hom.: 108 Cov.: 32 AF XY: 0.0281 AC XY: 2088 AN XY: 74388

African (AFR) AF: 0.0546 AC: 2268 AN: 41506

American (AMR) AF: 0.0208 AC: 318 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3468

East Asian (EAS) AF: 0.0697 AC: 359 AN: 5152

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4818

European-Finnish (FIN) AF: 0.0111 AC: 118 AN: 10608

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.00935 AC: 636 AN: 68010

Other (OTH) AF: 0.0322 AC: 68 AN: 2110

Alfa AF: 0.0215 Hom.: 12

Bravo AF: 0.0285

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.092
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: rs12618360; hg19: chr2-138013073;