rs8027411

Variant names:

• chr15-79168687-G-T
• rs8027411
• ENST00000671603.2:n.343-2975C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671603.2(ANKRD34C-AS1):​n.343-2975C>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 ENST00000671603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 27 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000671603.2	n.343-2975C>A		intron_variant	Intron 2 of 3
ANKRD34C-AS1	ENST00000685737.2	n.320-44001C>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

African (AFR) AF: 0.521 AC: 21613 AN: 41470

American (AMR) AF: 0.650 AC: 9934 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3468

East Asian (EAS) AF: 0.581 AC: 3006 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1412 AN: 4808

European-Finnish (FIN) AF: 0.537 AC: 5666 AN: 10554

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.508 AC: 34548 AN: 67970

Other (OTH) AF: 0.508 AC: 1069 AN: 2106

Alfa AF: 0.521 Hom.: 27308

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs8027411; hg19: chr15-79461029;