rs1474256

Variant names:

• chr15-79171505-C-T
• rs1474256
• ENST00000671603.2:n.343-5793G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671603.2(ANKRD34C-AS1):​n.343-5793G>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 ENST00000671603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 14 publications found

Genes affected

ANKRD34C-AS1 (HGNC:48618): (ANKRD34C antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671603.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD34C-AS1	ENST00000671603.2		n.343-5793G>A		intron	N/A
	ANKRD34C-AS1	ENST00000685737.2		n.320-46819G>A		intron	N/A
	ANKRD34C-AS1	ENST00000689461.1		n.376-5793G>A		intron	N/A

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

African (AFR) AF: 0.289 AC: 11985 AN: 41504

American (AMR) AF: 0.471 AC: 7201 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2646 AN: 5160

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4816

European-Finnish (FIN) AF: 0.411 AC: 4346 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28146 AN: 67968

Other (OTH) AF: 0.386 AC: 815 AN: 2110

Alfa AF: 0.407 Hom.: 30718

Bravo AF: 0.393

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1474256; hg19: chr15-79463847;