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GeneBe

rs737865

chr22-19942598-A-Gchr22-19942598-A-T

Variant summary

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

The NM_000754.4(COMT):c.-92+701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151968 control chromosomes in the gnomAD Genomes database, including 4398 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 0.23 ( 4398 hom., cov: 32)

Consequence

COMT
NM_000754.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.200

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COMTNM_000754.4 linkuse as main transcriptc.-92+701A>G intron_variant ENST00000361682.11
COMTNM_001362828.2 linkuse as main transcriptc.-386+701A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COMTENST00000361682.11 linkuse as main transcriptc.-92+701A>G intron_variant 1 NM_000754.4 P2P21964-1

Frequencies

GnomAD3 genomes
AF:
0.233
AC:
35389
AN:
151968
Hom.:
4398
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.149
Gnomad AMI
AF:
0.166
Gnomad AMR
AF:
0.220
Gnomad ASJ
AF:
0.427
Gnomad EAS
AF:
0.274
Gnomad SAS
AF:
0.263
Gnomad FIN
AF:
0.187
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.278
Gnomad OTH
AF:
0.256
Alfa
AF:
0.281
Hom.:
6729
Bravo
AF:
0.228
Asia WGS
AF:
0.271
AC:
944
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
6.4
Dann
Benign
0.79
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs737865; hg19: chr22-19930121;