ENST00000671603.1:n.318-5793G>A

Variant names:

• chr15-79171505-C-T
• rs1474256
• ENST00000671603.1:n.318-5793G>A

Variant summary

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

The ENST00000671603.1(ANKRD34C-AS1):​n.318-5793G>A variant causes a intron 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 ENST00000671603.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000671603.1	n.318-5793G>A		intron_variant	Intron 2 of 3
ANKRD34C-AS1	ENST00000685737.1	n.317-46819G>A		intron_variant	Intron 1 of 1
ANKRD34C-AS1	ENST00000689461.1	n.376-5793G>A		intron_variant	Intron 2 of 3

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;