rs1474256

Positions:

• chr15-79171505-C-T

Variant summary

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

The ENST00000685737.1(ANKRD34C-AS1):​n.317-46819G>A 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 0.381 in 152,078 control chromosomes in the GnomAD database, including 11,549 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 0.38 (11549 hom., cov: 32)
• Consequence: ANKRD34C-AS1 ENST00000685737.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000685737.1	n.317-46819G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57914 AN: 151960 Hom.: 11540 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.381 AC: 57961 AN: 152078 Hom.: 11549 Cov.: 32 AF XY: 0.382 AC XY: 28386 AN XY: 74324

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.386

Alfa AF: 0.414 Hom.: 20205

Bravo AF: 0.393

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1474256; hg19: chr15-79463847;