rs4779031

Positions:

• chr15-79241030-C-A
• chr15-79241030-C-T

Variant summary

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

The NR_038997.1(ANKRD34C-AS1):​n.297+42619G>T 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 0.666 in 151,460 control chromosomes in the GnomAD database, including 36,229 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 0.67 (36229 hom., cov: 28)
• Consequence: ANKRD34C-AS1 NR_038997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD34C-AS1	NR_038997.1	n.297+42619G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.316+42619G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.667 AC: 100907 AN: 151342 Hom.: 36241 Cov.: 28

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.666 AC: 100911 AN: 151460 Hom.: 36229 Cov.: 28 AF XY: 0.671 AC XY: 49652 AN XY: 73956

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.699

Alfa AF: 0.769 Hom.: 95020

Bravo AF: 0.643

Asia WGS AF: 0.703 AC: 2443 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4779031; hg19: chr15-79533372;