2-137118385-A-G

Variant names:

• chr2-137118385-A-G
• rs1469621
• NM_001316349.2:c.1369+3092A>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.1369+3092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,130 control chromosomes in the GnomAD database, including 10,971 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 0.34 (10971 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	NM_001316349.2	MANE Select	c.1369+3092A>G		intron	N/A	NP_001303278.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	ENST00000409968.6	TSL:5 MANE Select	c.1369+3092A>G		intron	N/A	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51806 AN: 152010 Hom.: 10977 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.340 AC: 51796 AN: 152130 Hom.: 10971 Cov.: 32 AF XY: 0.342 AC XY: 25406 AN XY: 74360

African (AFR) AF: 0.113 AC: 4701 AN: 41536

American (AMR) AF: 0.327 AC: 5002 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.133 AC: 688 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1247 AN: 4824

European-Finnish (FIN) AF: 0.552 AC: 5827 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31816 AN: 67964

Other (OTH) AF: 0.341 AC: 721 AN: 2114

Alfa AF: 0.397 Hom.: 24494

Bravo AF: 0.312

Asia WGS AF: 0.186 AC: 650 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.63
PhyloP100		-0.33
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: rs1469621; hg19: chr2-137875955;