rs8027411

Variant names:

• chr15-79168687-G-T
• rs8027411
• ENST00000671603.1:n.318-2975C>A

Variant summary

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

The ENST00000671603.1(ANKRD34C-AS1):​n.318-2975C>A variant causes a intron 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 ENST00000671603.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000671603.1	n.318-2975C>A		intron_variant	Intron 2 of 3
ANKRD34C-AS1	ENST00000685737.1	n.317-44001C>A		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000689461.1	n.376-2975C>A		intron_variant	Intron 2 of 3

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;