rs2224003

Variant summary

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

The 6-94446700-C-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,026 control chromosomes in the GnomAD database, including 2,703 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 0.17 ( 2703 hom., cov: 32)
Exomes 𝑓: 0.19 ( 0 hom. )

Consequence

MTCYBP36
ENST00000404146.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.393
Variant links:
Genes affected
MTCYBP36 (HGNC:52304): (MT-CYB pseudogene 36)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTCYBP36ENST00000404146.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25302
AN:
151892
Hom.:
2703
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0586
Gnomad AMI
AF:
0.360
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.236
Gnomad EAS
AF:
0.0136
Gnomad SAS
AF:
0.0824
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.236
Gnomad OTH
AF:
0.176
GnomAD4 exome
AF:
0.188
AC:
3
AN:
16
Hom.:
0
Cov.:
0
AF XY:
0.300
AC XY:
3
AN XY:
10
show subpopulations
Gnomad4 NFE exome
AF:
0.188
GnomAD4 genome
AF:
0.166
AC:
25289
AN:
152010
Hom.:
2703
Cov.:
32
AF XY:
0.163
AC XY:
12085
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.0584
Gnomad4 AMR
AF:
0.182
Gnomad4 ASJ
AF:
0.236
Gnomad4 EAS
AF:
0.0136
Gnomad4 SAS
AF:
0.0820
Gnomad4 FIN
AF:
0.194
Gnomad4 NFE
AF:
0.236
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.208
Hom.:
1688
Bravo
AF:
0.163
Asia WGS
AF:
0.0500
AC:
175
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.7
DANN
Benign
0.54

Splicing

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: rs2224003; hg19: chr6-95156418; COSMIC: COSV68189132; API