NM_001316349.2:c.3799+2700A>G

Variant names:

• chr2-137623426-A-G
• rs9678181
• NM_001316349.2:c.3799+2700A>G

Variant summary

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

The NM_001316349.2(THSD7B):​c.3799+2700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,916 control chromosomes in the GnomAD database, including 12,868 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 0.38 (12868 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 1 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001316349.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	NM_001316349.2	MANE Select	c.3799+2700A>G		intron	N/A	NP_001303278.1	Q9C0I4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	ENST00000409968.6	TSL:5 MANE Select	c.3799+2700A>G		intron	N/A	ENSP00000387145.1	Q9C0I4

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57417 AN: 151800 Hom.: 12835 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.379 AC: 57508 AN: 151916 Hom.: 12868 Cov.: 32 AF XY: 0.378 AC XY: 28059 AN XY: 74258

African (AFR) AF: 0.630 AC: 26055 AN: 41344

American (AMR) AF: 0.288 AC: 4405 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3468

East Asian (EAS) AF: 0.129 AC: 668 AN: 5162

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3246 AN: 10582

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19299 AN: 67956

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.345 Hom.: 1207

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.51
PhyloP100		-0.86
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: rs9678181; hg19: chr2-138380996;