chr15-79168687-G-T

Position:

• chr15-79168687-G-T

Variant summary

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

The ENST00000685737.1(ANKRD34C-AS1):​n.317-44001C>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 0.523 in 152,038 control chromosomes in the GnomAD database, including 21,038 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 0.52 (21038 hom., cov: 32)
• Consequence: ANKRD34C-AS1 ENST00000685737.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.317-44001C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79375 AN: 151920 Hom.: 21004 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.523 AC: 79463 AN: 152038 Hom.: 21038 Cov.: 32 AF XY: 0.524 AC XY: 38941 AN XY: 74316

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.508

Alfa AF: 0.516 Hom.: 20722

Bravo AF: 0.540

Asia WGS AF: 0.388 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8027411; hg19: chr15-79461029;