rs12210761

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_170155.1(OFCC1):​n.232-16304C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 152,224 control chromosomes in the GnomAD database, including 103 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 0.037 ( 103 hom., cov: 33)

Consequence

OFCC1
NR_170155.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.989
Variant links:
Genes affected

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=-0.68).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0374 (5692/152224) while in subpopulation SAS AF= 0.0449 (217/4828). AF 95% confidence interval is 0.0417. There are 103 homozygotes in gnomad4. There are 2722 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 103 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OFCC1NR_170155.1 linkuse as main transcriptn.232-16304C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000462111.1 linkuse as main transcriptn.164-16304C>T intron_variant, non_coding_transcript_variant 1
ENST00000481704.1 linkuse as main transcriptn.232-16304C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0373
AC:
5681
AN:
152106
Hom.:
101
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0363
Gnomad AMI
AF:
0.0395
Gnomad AMR
AF:
0.0216
Gnomad ASJ
AF:
0.0300
Gnomad EAS
AF:
0.0372
Gnomad SAS
AF:
0.0443
Gnomad FIN
AF:
0.0300
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0429
Gnomad OTH
AF:
0.0288
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0374
AC:
5692
AN:
152224
Hom.:
103
Cov.:
33
AF XY:
0.0366
AC XY:
2722
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0362
Gnomad4 AMR
AF:
0.0216
Gnomad4 ASJ
AF:
0.0300
Gnomad4 EAS
AF:
0.0375
Gnomad4 SAS
AF:
0.0449
Gnomad4 FIN
AF:
0.0300
Gnomad4 NFE
AF:
0.0429
Gnomad4 OTH
AF:
0.0294
Alfa
AF:
0.0379
Hom.:
168
Bravo
AF:
0.0356
Asia WGS
AF:
0.0430
AC:
150
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
10
DANN
Benign
0.72

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: rs12210761; hg19: chr6-10176036; API