15-79171618-C-T

Variant names:

• chr15-79171618-C-T
• rs17175798
• ENST00000671603.2:n.343-5906G>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.343-5906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,130 control chromosomes in the GnomAD database, including 13,542 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 0.40 (13542 hom., cov: 32)
• Consequence: ANKRD34C-AS1 ENST00000671603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 14 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 (SAS) allele frequency at 95% confidence interval = 0.684 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.343-5906G>A		intron_variant	Intron 2 of 3
ANKRD34C-AS1	ENST00000685737.2	n.320-46932G>A		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000689461.1	n.376-5906G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60982 AN: 152012 Hom.: 13546 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.401 AC: 60968 AN: 152130 Hom.: 13542 Cov.: 32 AF XY: 0.402 AC XY: 29882 AN XY: 74390

African (AFR) AF: 0.220 AC: 9119 AN: 41520

American (AMR) AF: 0.321 AC: 4911 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2145 AN: 5174

South Asian (SAS) AF: 0.704 AC: 3387 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4894 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33179 AN: 67964

Other (OTH) AF: 0.431 AC: 913 AN: 2116

Alfa AF: 0.303 Hom.: 1140

Bravo AF: 0.372

Asia WGS AF: 0.586 AC: 2038 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	1.6
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17175798; hg19: chr15-79463960;