rs8024156

chr15-79281062-G-A

Variant summary

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

The NR_038997.1(ANKRD34C-AS1):n.297+2587C>T 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 0.47 in 151,962 control chromosomes in the GnomAD database, including 17,595 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 0.47 (17595 hom., cov: 33)
• Consequence: ANKRD34C-AS1 NR_038997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD34C-AS1	NR_038997.1	n.297+2587C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.316+2587C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71467 AN: 151844 Hom.: 17592 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.470 AC: 71490 AN: 151962 Hom.: 17595 Cov.: 33 AF XY: 0.471 AC XY: 35005 AN XY: 74292

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.487

Alfa AF: 0.537 Hom.: 8700

Bravo AF: 0.455

Asia WGS AF: 0.396 AC: 1373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.5
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8024156; hg19: chr15-79573404;