rs4779031

Variant names:

• chr15-79241030-C-A
• rs4779031
• ENST00000557790.6:n.513-4102G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000557790.6(ANKRD34C-AS1):​n.513-4102G>T variant causes a intron 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 ENST00000557790.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557790.6. 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
	ANKRD34C-AS1	NR_038997.1		n.297+42619G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD34C-AS1	ENST00000557790.6	TSL:3	n.513-4102G>T		intron	N/A
	ANKRD34C-AS1	ENST00000558297.2	TSL:4	n.535-4102G>T		intron	N/A
	ANKRD34C-AS1	ENST00000559225.3	TSL:4	n.298-27671G>T		intron	N/A

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

African (AFR) AF: 0.378 AC: 15577 AN: 41248

American (AMR) AF: 0.674 AC: 10265 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2691 AN: 3466

East Asian (EAS) AF: 0.788 AC: 4010 AN: 5086

South Asian (SAS) AF: 0.742 AC: 3546 AN: 4776

European-Finnish (FIN) AF: 0.839 AC: 8762 AN: 10438

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53664 AN: 67892

Other (OTH) AF: 0.699 AC: 1474 AN: 2110

Alfa AF: 0.752 Hom.: 198557

Bravo AF: 0.643

Asia WGS AF: 0.703 AC: 2443 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.53
PhyloP100		0.030

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4779031;

hg19: chr15-79533372;