rs574135

Variant names:

• chr2-136982550-A-G
• rs574135
• NM_001316349.2:c.140-73870A>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.140-73870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,034 control chromosomes in the GnomAD database, including 19,281 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 0.49 (19281 hom., cov: 31)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.140-73870A>G		intron_variant	Intron 2 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-284-73870A>G		intron_variant	Intron 2 of 27		XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.140-73870A>G		intron_variant	Intron 2 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.*106-73870A>G		intron_variant	Intron 3 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73810 AN: 151916 Hom.: 19286 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.486 AC: 73830 AN: 152034 Hom.: 19281 Cov.: 31 AF XY: 0.485 AC XY: 36044 AN XY: 74314

African (AFR) AF: 0.348 AC: 14453 AN: 41472

American (AMR) AF: 0.402 AC: 6139 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1782 AN: 3472

East Asian (EAS) AF: 0.180 AC: 932 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4822

European-Finnish (FIN) AF: 0.682 AC: 7187 AN: 10540

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39814 AN: 67968

Other (OTH) AF: 0.457 AC: 966 AN: 2112

Alfa AF: 0.532 Hom.: 54880

Bravo AF: 0.458

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.32
PhyloP100		-0.088
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: rs574135; hg19: chr2-137740120;