15-79209525-T-G

Variant names:

• chr15-79209525-T-G
• rs12324079
• ENST00000711326.1:n.123T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000711326.1(ENSG00000292375):​n.123T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,130 control chromosomes in the GnomAD database, including 16,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (16351 hom., cov: 33)
• Consequence: ENSG00000292375 ENST00000711326.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0680
• Publications: 3 publications found

Genes affected

ENSG00000292375 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 15-79209525-T-G is Benign according to our data. Variant chr15-79209525-T-G is described in ClinVar as Benign. ClinVar VariationId is 1249129.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711326.1. 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.298-17423A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000292375	ENST00000711326.1		n.123T>G		non_coding_transcript_exon	Exon 1 of 2
	ANKRD34C-AS1	ENST00000559225.3	TSL:4	n.470+3662A>C		intron	N/A
	ANKRD34C-AS1	ENST00000560872.1	TSL:3	n.178-17423A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66750 AN: 152012 Hom.: 16345 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.439 AC: 66765 AN: 152130 Hom.: 16351 Cov.: 33 AF XY: 0.443 AC XY: 32917 AN XY: 74362

African (AFR) AF: 0.206 AC: 8545 AN: 41516

American (AMR) AF: 0.548 AC: 8385 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2017 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2858 AN: 5168

South Asian (SAS) AF: 0.405 AC: 1950 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5646 AN: 10566

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35747 AN: 67982

Other (OTH) AF: 0.477 AC: 1009 AN: 2114

Alfa AF: 0.499 Hom.: 53394

Bravo AF: 0.438

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.67
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs12324079; hg19: chr15-79501867;