rs347882

Variant names:

• chr15-34382125-C-A
• rs347882
• NM_181077.5:c.1352+26G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34382125-C-A
• chr15-34382125-C-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_181077.5(GOLGA8A):​c.1352+26G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
  • Exomes 𝑓: 0.000044 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8A NM_181077.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 5 publications found

Genes affected

GOLGA8A (HGNC:31972): (golgin A8 family member A) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked, flattened membrane sacs referred to as cisternae. Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. The golgins constitute a family of proteins which are localized to the Golgi. This gene encodes a golgin which structurally resembles its family member GOLGA2, suggesting that they may share a similar function. There are many similar copies of this gene on chromosome 15. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

MIR1233-1 (HGNC:33929): (microRNA 1233-1) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8A	NM_181077.5	c.1352+26G>T		intron_variant	Intron 22 of 24	ENST00000359187.5	NP_851422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8A	ENST00000359187.5	c.1352+26G>T		intron_variant	Intron 22 of 24	1	NM_181077.5	ENSP00000352111.4
GOLGA8A	ENST00000473125.5	n.3430+26G>T		intron_variant	Intron 20 of 22	1
MIR1233-1	ENST00000408722.1	n.26G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
GOLGA8A	ENST00000699472.1	c.1349+26G>T		intron_variant	Intron 22 of 24			ENSP00000514395.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.000118 AC: 3 AN: 25376 AF XY: 0.000152

Gnomad AFR exome AF: 0.000266

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000108

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000444 AC: 7 AN: 157756 Hom.: 0 Cov.: 0 AF XY: 0.0000364 AC XY: 3 AN XY: 82396

African (AFR) AF: 0.00 AC: 0 AN: 6852

American (AMR) AF: 0.000108 AC: 1 AN: 9250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5292

East Asian (EAS) AF: 0.00 AC: 0 AN: 6502

South Asian (SAS) AF: 0.00 AC: 0 AN: 22912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7980

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 662

European-Non Finnish (NFE) AF: 0.0000558 AC: 5 AN: 89544

Other (OTH) AF: 0.000114 AC: 1 AN: 8762

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.48
PhyloP100		-0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs347882; hg19: chr15-34674326;