ENST00000559225.2:n.436+3662A>C

Variant names:

• chr15-79209525-T-G
• rs12324079
• ENST00000559225.2:n.436+3662A>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000559225.2(ANKRD34C-AS1):​n.436+3662A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,130 control chromosomes in the GnomAD database, including 16,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (16351 hom., cov: 33)
• Consequence: ANKRD34C-AS1 ENST00000559225.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0680

Genes affected

ANKRD34C-AS1 (HGNC:48618): (ANKRD34C antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 15-79209525-T-G is Benign according to our data. Variant chr15-79209525-T-G is described in ClinVar as [Benign]. Clinvar id is 1249129.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD34C-AS1	NR_038997.1	n.298-17423A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000559225.2	n.436+3662A>C		intron_variant	Intron 2 of 2	4
ANKRD34C-AS1	ENST00000560872.1	n.178-17423A>C		intron_variant	Intron 1 of 1	3
ANKRD34C-AS1	ENST00000661423.1	n.339-17423A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66750 AN: 152012 Hom.: 16345 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.439 AC: 66765 AN: 152130 Hom.: 16351 Cov.: 33 AF XY: 0.443 AC XY: 32917 AN XY: 74362

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.477

Alfa AF: 0.515 Hom.: 19657

Bravo AF: 0.438

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12324079; hg19: chr15-79501867;