15-79163008-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685737.1(ANKRD34C-AS1):n.317-38322G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,942 control chromosomes in the GnomAD database, including 20,362 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 0.51 (20362 hom., cov: 32)
• Consequence: ANKRD34C-AS1 ENST00000685737.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.317-38322G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78013 AN: 151824 Hom.: 20337 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.514 AC: 78082 AN: 151942 Hom.: 20362 Cov.: 32 AF XY: 0.516 AC XY: 38275 AN XY: 74236

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.507

Alfa AF: 0.497 Hom.: 7796

Bravo AF: 0.530

Asia WGS AF: 0.378 AC: 1313 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.8
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8033963; hg19: chr15-79455350;