Variant chr7-11375812-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_015204.3(THSD7A):c.4956T>C(p.Asp1652=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00525 in 1,612,644 control chromosomes in the GnomAD database, including 251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 130 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 121 hom. )

Consequence

THSD7A
NM_015204.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.88

Variant links:

Genes affected

THSD7A (HGNC:22207): (thrombospondin type 1 domain containing 7A) The protein encoded by this gene is found almost exclusively in endothelial cells from placenta and umbilical cord. The encoded protein appears to interact with alpha(V)beta(3) integrin and paxillin to inhibit endothelial cell migration and tube formation. This protein may be involved in cytoskeletal organization. Variations in this gene may be associated with low bone mineral density in osteoporosis. [provided by RefSeq, Aug 2010]

THSD7A links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 7-11375812-A-G is Benign according to our data. Variant chr7-11375812-A-G is described in ClinVar as [Benign]. Clinvar id is 775247.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.88 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THSD7A	NM_015204.3 linkuse as main transcript	c.4956T>C	p.Asp1652=	synonymous_variant	28/28	ENST00000423059.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THSD7A	ENST00000423059.9 linkuse as main transcript	c.4956T>C	p.Asp1652=	synonymous_variant	28/28	5	NM_015204.3	P1
	ENST00000445839.5 linkuse as main transcript	n.247-3475A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0225

AC:

3414

AN:

152062

Hom.:

127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0156

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00703

AC:

1748

AN:

248708

Hom.:

AF XY:

0.00576

AC XY:

777

AN XY:

134924

show subpopulations

Gnomad AFR exome

AF:

0.0767

Gnomad AMR exome

AF:

0.00839

Gnomad ASJ exome

AF:

0.000797

Gnomad EAS exome

AF:

0.000390

Gnomad SAS exome

AF:

0.000295

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00187

Gnomad OTH exome

AF:

0.00614

GnomAD4 exome

AF:

0.00345

AC:

5033

AN:

1460464

Hom.:

121

Cov.:

AF XY:

0.00315

AC XY:

2289

AN XY:

726514

show subpopulations

Gnomad4 AFR exome

AF:

0.0797

Gnomad4 AMR exome

AF:

0.00897

Gnomad4 ASJ exome

AF:

0.000690

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.000278

Gnomad4 FIN exome

AF:

0.0000749

Gnomad4 NFE exome

AF:

0.00121

Gnomad4 OTH exome

AF:

0.00796

GnomAD4 genome

AF:

0.0225

AC:

3431

AN:

152180

Hom.:

130

Cov.:

AF XY:

0.0219

AC XY:

1633

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0730

Gnomad4 AMR

AF:

0.0157

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.0118

Hom.:

Bravo

AF:

0.0261

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.00164

EpiControl

AF:

0.00220

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

6.3

DANN

Benign

0.71

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over