rs939661

Positions:

• chr15-79138721-A-G
• chr15-79138721-A-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.317-14035T>C		intron_variant, non_coding_transcript_variant

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;