rs530525459

Variant names:

• chr15-23360525-C-A
• rs530525459
• NM_001395373.1:c.818C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-23360525-C-A
• chr15-23360525-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001395373.1(GOLGA8S):​c.818C>A​(p.Ser273*) variant causes a stop gained 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. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.000047 (0 hom., cov: 27)
  • Exomes 𝑓: 0.000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8S NM_001395373.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

GOLGA8S (HGNC:44409): (golgin A8 family member S) Predicted to be involved in Golgi organization. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8S	NM_001395373.1	c.818C>A	p.Ser273*	stop_gained	Exon 10 of 19	ENST00000562295.3	NP_001382302.1
GOLGA8S	NM_001355465.2	c.140C>A	p.Ser47*	stop_gained	Exon 9 of 18		NP_001342394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8S	ENST00000562295.3	c.818C>A	p.Ser273*	stop_gained	Exon 10 of 19	5	NM_001395373.1	ENSP00000455298.2
GOLGA8S	ENST00000604046.1	n.1153C>A		non_coding_transcript_exon_variant	Exon 9 of 18	1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 7 AN: 147838 Hom.: 0 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000473

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000921 AC: 6 AN: 65178 Hom.: 0 AF XY: 0.000155 AC XY: 5 AN XY: 32310

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000546

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000209 AC: 14 AN: 668656 Hom.: 0 Cov.: 8 AF XY: 0.0000222 AC XY: 8 AN XY: 360662

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000302

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000292

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000473 AC: 7 AN: 147838 Hom.: 0 Cov.: 27 AF XY: 0.0000556 AC XY: 4 AN XY: 71968

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000473

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.087	T
BayesDel_noAF	Uncertain	-0.010
CADD	Pathogenic	28
DANN	Benign	0.94
FATHMM_MKL	Benign	0.025	N
Vest4		0.045
GERP RS		-0.15

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

Publications

LitVar

Other links and lift over

dbSNP: rs530525459; hg19: chr15-23605672;