15-79159527-A-G

Variant names:

• chr15-79159527-A-G
• rs939658
• ENST00000671603.2:n.438+6090T>C

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+6090T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,978 control chromosomes in the GnomAD database, including 21,403 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 0.53 (21403 hom., cov: 31)
• Consequence: ANKRD34C-AS1 ENST00000671603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 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.438+6090T>C		intron_variant	Intron 3 of 3
ANKRD34C-AS1	ENST00000685737.2	n.320-34841T>C		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000689461.1	n.471+6090T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80018 AN: 151860 Hom.: 21371 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.527 AC: 80102 AN: 151978 Hom.: 21403 Cov.: 31 AF XY: 0.528 AC XY: 39230 AN XY: 74288

African (AFR) AF: 0.532 AC: 22045 AN: 41438

American (AMR) AF: 0.652 AC: 9961 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1706 AN: 3472

East Asian (EAS) AF: 0.593 AC: 3056 AN: 5152

South Asian (SAS) AF: 0.297 AC: 1429 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5665 AN: 10566

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34622 AN: 67954

Other (OTH) AF: 0.518 AC: 1096 AN: 2114

Alfa AF: 0.519 Hom.: 63658

Bravo AF: 0.545

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs939658; hg19: chr15-79451869;