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GeneBe

rs7578597

chr2-43505684-T-C

Variant summary

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

The NM_022065.5(THADA):c.3559A>G(p.Thr1187Ala) variant causes a missense change. The variant allele was found at a frequency of 0.14 in 152144 control chromosomes in the gnomAD Genomes database, including 1986 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1986 hom., cov: 32)
Exomes 𝑓: 0.099 ( 1424 hom. )

Consequence

THADA
NM_022065.5 missense

Scores

5
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.85

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.0019688606).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
THADANM_022065.5 linkuse as main transcriptc.3559A>G p.Thr1187Ala missense_variant 24/38 ENST00000405975.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
THADAENST00000405975.7 linkuse as main transcriptc.3559A>G p.Thr1187Ala missense_variant 24/381 NM_022065.5 P1Q6YHU6-1

Frequencies

GnomAD3 genomes
AF:
0.140
AC:
21313
AN:
152144
Hom.:
1986
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.264
Gnomad AMI
AF:
0.0669
Gnomad AMR
AF:
0.0812
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.00672
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.0481
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.106
Gnomad OTH
AF:
0.113
GnomAD3 exomes
AF:
0.0990
AC:
21766
AN:
219906
Hom.:
1424
AF XY:
0.100
AC XY:
11828
AN XY:
117810
show subpopulations
Gnomad AFR exome
AF:
0.268
Gnomad AMR exome
AF:
0.0564
Gnomad ASJ exome
AF:
0.118
Gnomad EAS exome
AF:
0.00576
Gnomad SAS exome
AF:
0.134
Gnomad FIN exome
AF:
0.0510
Gnomad NFE exome
AF:
0.104
Gnomad OTH exome
AF:
0.0960
GnomAD4 exome
AF:
0.106
AC:
153003
AN:
1441586
Hom.:
9115
AF XY:
0.107
AC XY:
76205
AN XY:
714672
show subpopulations
Gnomad4 AFR exome
AF:
0.268
Gnomad4 AMR exome
AF:
0.0585
Gnomad4 ASJ exome
AF:
0.118
Gnomad4 EAS exome
AF:
0.00779
Gnomad4 SAS exome
AF:
0.135
Gnomad4 FIN exome
AF:
0.0530
Gnomad4 NFE exome
AF:
0.107
Gnomad4 OTH exome
AF:
0.100
Alfa
AF:
0.110
Hom.:
2592
Bravo
AF:
0.146
TwinsUK
AF:
0.107
AC:
398
ALSPAC
AF:
0.115
AC:
444
ESP6500AA
AF:
0.260
AC:
968
ESP6500EA
AF:
0.110
AC:
897
ExAC
AF:
0.0971
AC:
11681
Asia WGS
AF:
0.0660
AC:
231
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.33
Cadd
Uncertain
24
Dann
Uncertain
0.99
DEOGEN2
Benign
0.014
T;T
Eigen
Uncertain
0.23
Eigen_PC
Uncertain
0.35
FATHMM_MKL
Uncertain
0.95
D
MetaRNN
Benign
0.0020
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;L
MutationTaster
Benign
0.00085
P;P;P;P
PrimateAI
Uncertain
0.51
T
PROVEAN
Benign
-1.7
N;N
REVEL
Benign
0.094
Sift
Benign
0.089
T;T
Sift4G
Benign
0.080
T;T
Polyphen
0.17
B;B
Vest4
0.15
ClinPred
0.014
T
GERP RS
5.5
Varity_R
0.26
gMVP
0.52

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: rs7578597; hg19: chr2-43732823; COSMIC: COSV57682006; COSMIC: COSV57682006;