16-82090913-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002153.3(HSD17B2):c.676A>G(p.Met226Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00876 in 1,611,502 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0089 ( 86 hom. )
Consequence
HSD17B2
NM_002153.3 missense
NM_002153.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.270
Genes affected
HSD17B2 (HGNC:5211): (hydroxysteroid 17-beta dehydrogenase 2) Enables estradiol 17-beta-dehydrogenase activity and testosterone dehydrogenase (NAD+) activity. Involved in response to retinoic acid. Predicted to be located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005282551).
BP6
?
Variant 16-82090913-A-G is Benign according to our data. Variant chr16-82090913-A-G is described in ClinVar as [Benign]. Clinvar id is 787563.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD17B2 | NM_002153.3 | c.676A>G | p.Met226Val | missense_variant | 4/5 | ENST00000199936.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B2 | ENST00000199936.9 | c.676A>G | p.Met226Val | missense_variant | 4/5 | 1 | NM_002153.3 | P1 | |
HSD17B2-AS1 | ENST00000567021.1 | n.44-19724T>C | intron_variant, non_coding_transcript_variant | 5 | |||||
HSD17B2 | ENST00000568090.5 | c.268A>G | p.Met90Val | missense_variant | 4/5 | 3 | |||
HSD17B2 | ENST00000566838.2 | c.304A>G | p.Met102Val | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00755 AC: 1149AN: 152146Hom.: 8 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00742 AC: 1848AN: 249088Hom.: 13 AF XY: 0.00779 AC XY: 1048AN XY: 134582
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GnomAD4 exome AF: 0.00889 AC: 12974AN: 1459238Hom.: 86 Cov.: 31 AF XY: 0.00890 AC XY: 6456AN XY: 725722
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GnomAD4 genome ? AF: 0.00754 AC: 1148AN: 152264Hom.: 8 Cov.: 32 AF XY: 0.00746 AC XY: 555AN XY: 74442
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ESP6500AA
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ExAC
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950
Asia WGS
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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 | Invitae | Aug 15, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at