rs979976

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001316349.2(THSD7B):​c.140-45288A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,940 control chromosomes in the GnomAD database, including 29,159 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 0.60 ( 29159 hom., cov: 31)

Consequence

THSD7B
NM_001316349.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.820
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
THSD7BNM_001316349.2 linkuse as main transcriptc.140-45288A>C intron_variant ENST00000409968.6 NP_001303278.1
THSD7BXM_047445935.1 linkuse as main transcriptc.-284-45288A>C intron_variant XP_047301891.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
THSD7BENST00000409968.6 linkuse as main transcriptc.140-45288A>C intron_variant 5 NM_001316349.2 ENSP00000387145 P1
THSD7BENST00000472720.5 linkuse as main transcriptc.*106-45288A>C intron_variant, NMD_transcript_variant 5 ENSP00000473349

Frequencies

GnomAD3 genomes
AF:
0.603
AC:
91623
AN:
151822
Hom.:
29153
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.385
Gnomad AMI
AF:
0.785
Gnomad AMR
AF:
0.656
Gnomad ASJ
AF:
0.733
Gnomad EAS
AF:
0.643
Gnomad SAS
AF:
0.760
Gnomad FIN
AF:
0.768
Gnomad MID
AF:
0.709
Gnomad NFE
AF:
0.675
Gnomad OTH
AF:
0.624
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.603
AC:
91652
AN:
151940
Hom.:
29159
Cov.:
31
AF XY:
0.612
AC XY:
45443
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.385
Gnomad4 AMR
AF:
0.655
Gnomad4 ASJ
AF:
0.733
Gnomad4 EAS
AF:
0.644
Gnomad4 SAS
AF:
0.760
Gnomad4 FIN
AF:
0.768
Gnomad4 NFE
AF:
0.675
Gnomad4 OTH
AF:
0.623
Alfa
AF:
0.666
Hom.:
67041
Bravo
AF:
0.581
Asia WGS
AF:
0.681
AC:
2366
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.17
DANN
Benign
0.77

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.

Other links and lift over

dbSNP: rs979976; hg19: chr2-137768702; API