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rs6269

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000754(COMT):c.1-98A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152008 control chromosomes in the gnomAD Genomes database, including 10884 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 10884 hom., cov: 33)

Consequence

COMT
NM_000754 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.47

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 22:19962429-A>G is Benign according to our data. Variant chr22-19962429-A-G is described in ClinVar as [Benign]. Clinvar id is 1275060. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COMTNM_000754.4 linkuse as main transcriptc.1-98A>G intron_variant ENST00000361682.11
COMTNM_001362828.2 linkuse as main transcriptc.-98A>G 5_prime_UTR_variant 3/6
COMTNM_001135161.2 linkuse as main transcriptc.1-98A>G intron_variant
COMTNM_001135162.2 linkuse as main transcriptc.1-98A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COMTENST00000361682.11 linkuse as main transcriptc.1-98A>G intron_variant 1 NM_000754.4 P2P21964-1

Frequencies

GnomAD3 genomes
AF:
0.377
AC:
57285
AN:
152008
Hom.:
10884
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.375
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.331
Gnomad ASJ
AF:
0.475
Gnomad EAS
AF:
0.325
Gnomad SAS
AF:
0.330
Gnomad FIN
AF:
0.309
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.401
Gnomad OTH
AF:
0.396
GnomAD4 exome
AF:
0.392
AC:
536868
AN:
1369392
Hom.:
106561
AF XY:
0.392
AC XY:
263406
AN XY:
672754
show subpopulations
Gnomad4 AFR exome
AF:
0.368
Gnomad4 AMR exome
AF:
0.244
Gnomad4 ASJ exome
AF:
0.462
Gnomad4 EAS exome
AF:
0.295
Gnomad4 SAS exome
AF:
0.339
Gnomad4 FIN exome
AF:
0.325
Gnomad4 NFE exome
AF:
0.405
Gnomad4 OTH exome
AF:
0.397
Alfa
AF:
0.376
Hom.:
3423
Bravo
AF:
0.378
Asia WGS
AF:
0.327
AC:
1141
AN:
3478

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 submitterclinical testingGeneDxMay 10, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.51
Dann
Benign
0.39

Splicing

Find out SpliceAI 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: rs6269; hg19: chr22-19949952; COSMIC: COSV52891062; COSMIC: COSV52891062;