rs12903401

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000560872.1(ANKRD34C-AS1):​n.178-17652C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 501,760 control chromosomes in the GnomAD database, including 52,598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13946 hom., cov: 32)
Exomes 𝑓: 0.46 ( 38652 hom. )

Consequence

ANKRD34C-AS1
ENST00000560872.1 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.402
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 15-79209754-G-C is Benign according to our data. Variant chr15-79209754-G-C is described in ClinVar as [Benign]. Clinvar id is 1223338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANKRD34C-AS1NR_038997.1 linkuse as main transcriptn.298-17652C>G intron_variant
MIR184NR_029705.1 linkuse as main transcriptn.-34G>C upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANKRD34C-AS1ENST00000559225.2 linkuse as main transcriptn.436+3433C>G intron_variant 4
ANKRD34C-AS1ENST00000560872.1 linkuse as main transcriptn.178-17652C>G intron_variant 3
ANKRD34C-AS1ENST00000661423.1 linkuse as main transcriptn.339-17652C>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.406
AC:
61592
AN:
151888
Hom.:
13937
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.197
Gnomad AMI
AF:
0.366
Gnomad AMR
AF:
0.526
Gnomad ASJ
AF:
0.489
Gnomad EAS
AF:
0.552
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.476
Gnomad MID
AF:
0.560
Gnomad NFE
AF:
0.481
Gnomad OTH
AF:
0.450
GnomAD3 exomes
AF:
0.464
AC:
115006
AN:
247820
Hom.:
27733
AF XY:
0.462
AC XY:
61934
AN XY:
134128
show subpopulations
Gnomad AFR exome
AF:
0.190
Gnomad AMR exome
AF:
0.542
Gnomad ASJ exome
AF:
0.507
Gnomad EAS exome
AF:
0.566
Gnomad SAS exome
AF:
0.358
Gnomad FIN exome
AF:
0.481
Gnomad NFE exome
AF:
0.483
Gnomad OTH exome
AF:
0.485
GnomAD4 exome
AF:
0.461
AC:
161409
AN:
349756
Hom.:
38652
Cov.:
0
AF XY:
0.453
AC XY:
89226
AN XY:
197054
show subpopulations
Gnomad4 AFR exome
AF:
0.199
Gnomad4 AMR exome
AF:
0.541
Gnomad4 ASJ exome
AF:
0.508
Gnomad4 EAS exome
AF:
0.570
Gnomad4 SAS exome
AF:
0.366
Gnomad4 FIN exome
AF:
0.480
Gnomad4 NFE exome
AF:
0.481
Gnomad4 OTH exome
AF:
0.463
GnomAD4 genome
AF:
0.405
AC:
61610
AN:
152004
Hom.:
13946
Cov.:
32
AF XY:
0.409
AC XY:
30358
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.196
Gnomad4 AMR
AF:
0.527
Gnomad4 ASJ
AF:
0.489
Gnomad4 EAS
AF:
0.553
Gnomad4 SAS
AF:
0.364
Gnomad4 FIN
AF:
0.476
Gnomad4 NFE
AF:
0.481
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.445
Hom.:
2931
Bravo
AF:
0.408
Asia WGS
AF:
0.420
AC:
1463
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJul 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
6.3
DANN
Benign
0.84

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: rs12903401; hg19: chr15-79502096; COSMIC: COSV66045224; API