rs12903401

Positions:

• chr15-79209754-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.402

Genes affected

ANKRD34C-AS1 (HGNC:):

ACMG classification

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-AS1	NR_038997.1	n.298-17652C>G		intron_variant
MIR184	NR_029705.1	n.-34G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000559225.2	n.436+3433C>G		intron_variant		4
ANKRD34C-AS1	ENST00000560872.1	n.178-17652C>G		intron_variant		3
ANKRD34C-AS1	ENST00000661423.1	n.339-17652C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61592 AN: 151888 Hom.: 13937 Cov.: 32

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

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

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

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

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.68
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

Other links and lift over

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