2-136855017-A-T

Variant summary

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

The NM_001316349.2(THSD7B):​c.-35-27127A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,110 control chromosomes in the GnomAD database, including 43,826 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 0.76 ( 43826 hom., cov: 32)

Consequence

THSD7B
NM_001316349.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.619
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=-1.02).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
THSD7BNM_001316349.2 linkuse as main transcriptc.-35-27127A>T intron_variant ENST00000409968.6 NP_001303278.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
THSD7BENST00000409968.6 linkuse as main transcriptc.-35-27127A>T intron_variant 5 NM_001316349.2 ENSP00000387145 P1
THSD7BENST00000472720.5 linkuse as main transcriptc.-35-27127A>T intron_variant, NMD_transcript_variant 5 ENSP00000473349

Frequencies

GnomAD3 genomes
AF:
0.757
AC:
115062
AN:
151992
Hom.:
43800
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.787
Gnomad AMI
AF:
0.688
Gnomad AMR
AF:
0.835
Gnomad ASJ
AF:
0.827
Gnomad EAS
AF:
0.729
Gnomad SAS
AF:
0.768
Gnomad FIN
AF:
0.701
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.728
Gnomad OTH
AF:
0.790
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.757
AC:
115143
AN:
152110
Hom.:
43826
Cov.:
32
AF XY:
0.758
AC XY:
56367
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.786
Gnomad4 AMR
AF:
0.835
Gnomad4 ASJ
AF:
0.827
Gnomad4 EAS
AF:
0.728
Gnomad4 SAS
AF:
0.769
Gnomad4 FIN
AF:
0.701
Gnomad4 NFE
AF:
0.728
Gnomad4 OTH
AF:
0.787
Alfa
AF:
0.751
Hom.:
5324
Bravo
AF:
0.770
Asia WGS
AF:
0.742
AC:
2580
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
0.63
DANN
Benign
0.37

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: rs1346731; hg19: chr2-137612587; API