chr15-79163008-C-T

Variant names:

• chr15-79163008-C-T
• rs8033963
• ENST00000671603.2:n.438+2609G>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.438+2609G>A variant causes a intron 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 ENST00000671603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671603.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD34C-AS1	ENST00000671603.2		n.438+2609G>A		intron	N/A
	ANKRD34C-AS1	ENST00000685737.2		n.320-38322G>A		intron	N/A
	ANKRD34C-AS1	ENST00000689461.1		n.471+2609G>A		intron	N/A

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

African (AFR) AF: 0.490 AC: 20318 AN: 41446

American (AMR) AF: 0.647 AC: 9884 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3016 AN: 5170

South Asian (SAS) AF: 0.291 AC: 1398 AN: 4804

European-Finnish (FIN) AF: 0.537 AC: 5663 AN: 10540

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34507 AN: 67928

Other (OTH) AF: 0.507 AC: 1069 AN: 2110

Alfa AF: 0.498 Hom.: 8852

Bravo AF: 0.530

Asia WGS AF: 0.378 AC: 1313 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.42
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs8033963; hg19: chr15-79455350;