ENST00000685737.1:n.317-14035T>C

Variant names:

• chr15-79138721-A-G
• rs939661
• ENST00000685737.1:n.317-14035T>C

Variant summary

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

The ENST00000685737.1(ANKRD34C-AS1):​n.317-14035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,904 control chromosomes in the GnomAD database, including 13,201 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 0.39 (13201 hom., cov: 31)
• Consequence: ANKRD34C-AS1 ENST00000685737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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	ENST00000685737.1	n.317-14035T>C		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000689752.2	n.305-14032T>C		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000692103.1	n.388-14035T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59443 AN: 151786 Hom.: 13202 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.391 AC: 59437 AN: 151904 Hom.: 13201 Cov.: 31 AF XY: 0.393 AC XY: 29148 AN XY: 74248

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.435

Alfa AF: 0.471 Hom.: 22548

Bravo AF: 0.363

Asia WGS AF: 0.566 AC: 1969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939661; hg19: chr15-79431063;