chr2-137010442-C-A

Variant names:

• chr2-137010442-C-A
• rs10928585
• NM_001316349.2:c.140-45978C>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.140-45978C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,140 control chromosomes in the GnomAD database, including 430 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 0.073 (430 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.140-45978C>A		intron_variant	Intron 2 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-284-45978C>A		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.140-45978C>A		intron_variant	Intron 2 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.*106-45978C>A		intron_variant	Intron 3 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11049 AN: 152022 Hom.: 430 Cov.: 33

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0727 AC: 11055 AN: 152140 Hom.: 430 Cov.: 33 AF XY: 0.0736 AC XY: 5475 AN XY: 74384

African (AFR) AF: 0.0638 AC: 2644 AN: 41474

American (AMR) AF: 0.0948 AC: 1449 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.147 AC: 759 AN: 5176

South Asian (SAS) AF: 0.0638 AC: 308 AN: 4828

European-Finnish (FIN) AF: 0.0588 AC: 622 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4757 AN: 68002

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0728 Hom.: 778

Bravo AF: 0.0768

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		-0.016
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: rs10928585; hg19: chr2-137768012;