Variant 15-79210027-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000560872.1(ANKRD34C-AS1):n.178-17925C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 150,654 control chromosomes in the GnomAD database, including 3,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 3330 hom., cov: 32)

Consequence

ANKRD34C-AS1
ENST00000560872.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.165

Variant links:

Genes affected

ANKRD34C-AS1 (HGNC:):

ANKRD34C-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 15-79210027-G-C is Benign according to our data. Variant chr15-79210027-G-C is described in ClinVar as [Benign]. Clinvar id is 1246314.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD34C-AS1	NR_038997.1 linkuse as main transcript	n.298-17925C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ANKRD34C-AS1	ENST00000559225.2 linkuse as main transcript	n.436+3160C>G	intron_variant	4
ANKRD34C-AS1	ENST00000560872.1 linkuse as main transcript	n.178-17925C>G	intron_variant	3
ANKRD34C-AS1	ENST00000661423.1 linkuse as main transcript	n.339-17925C>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17422

AN:

150536

Hom.:

3318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0413

Gnomad ASJ

AF:

0.00669

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00106

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0194

Gnomad NFE

AF:

0.00232

Gnomad OTH

AF:

0.0771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.116

AC:

17473

AN:

150654

Hom.:

3330

Cov.:

AF XY:

0.112

AC XY:

8226

AN XY:

73686

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.0413

Gnomad4 ASJ

AF:

0.00669

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00106

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00230

Gnomad4 OTH

AF:

0.0763

Alfa

AF:

0.0877

Hom.:

232

Bravo

AF:

0.131

Asia WGS

AF:

0.0200

AC:

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 submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.5

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over