2-216998758-C-G

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+4740C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,064 control chromosomes in the GnomAD database, including 6,615 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 0.25 ( 6615 hom., cov: 32)

Consequence

DIRC3-AS1
ENST00000695932.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DIRC3-AS1ENST00000695932.1 linkn.509+4740C>G intron_variant Intron 3 of 11
DIRC3-AS1ENST00000695934.1 linkn.172+4740C>G intron_variant Intron 3 of 8
DIRC3-AS1ENST00000695937.1 linkn.221+4740C>G intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38447
AN:
151946
Hom.:
6604
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.159
Gnomad EAS
AF:
0.834
Gnomad SAS
AF:
0.276
Gnomad FIN
AF:
0.336
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.262
Gnomad OTH
AF:
0.256
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.253
AC:
38474
AN:
152064
Hom.:
6615
Cov.:
32
AF XY:
0.261
AC XY:
19368
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.391
Gnomad4 ASJ
AF:
0.159
Gnomad4 EAS
AF:
0.834
Gnomad4 SAS
AF:
0.276
Gnomad4 FIN
AF:
0.336
Gnomad4 NFE
AF:
0.262
Gnomad4 OTH
AF:
0.258
Alfa
AF:
0.145
Hom.:
305
Bravo
AF:
0.257
Asia WGS
AF:
0.559
AC:
1939
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.1
DANN
Benign
0.49

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: rs10932688; hg19: chr2-217863481; API