rs2879515

Variant names:

• chr15-34579095-A-G
• rs2879515
• NM_001023567.5:c.-1123+4421T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-34579095-A-G
• chr15-34579095-A-T

Variant summary

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

The NM_001023567.5(GOLGA8B):​c.-1123+4421T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,682 control chromosomes in the GnomAD database, including 24,568 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 0.56 (24568 hom., cov: 30)
• Consequence: GOLGA8B NM_001023567.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 13 publications found

Genes affected

GOLGA8B (HGNC:31973): (golgin A8 family member B) Predicted to be involved in Golgi organization and spindle assembly. Located in Golgi apparatus and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8B	NM_001023567.5	c.-1123+4421T>C		intron_variant	Intron 1 of 23	ENST00000683415.1	NP_001018861.3
GOLGA8B	NR_027410.2	n.225+2371T>C		intron_variant	Intron 2 of 23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8B	ENST00000683415.1	c.-1123+4421T>C		intron_variant	Intron 1 of 23		NM_001023567.5	ENSP00000507830.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85129 AN: 151562 Hom.: 24519 Cov.: 30

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.562 AC: 85236 AN: 151682 Hom.: 24568 Cov.: 30 AF XY: 0.561 AC XY: 41587 AN XY: 74100

African (AFR) AF: 0.675 AC: 27910 AN: 41334

American (AMR) AF: 0.621 AC: 9467 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2058 AN: 3462

East Asian (EAS) AF: 0.473 AC: 2416 AN: 5108

South Asian (SAS) AF: 0.509 AC: 2441 AN: 4798

European-Finnish (FIN) AF: 0.532 AC: 5580 AN: 10498

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33664 AN: 67926

Other (OTH) AF: 0.561 AC: 1183 AN: 2110

Alfa AF: 0.517 Hom.: 84572

Bravo AF: 0.580

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.18
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2879515; hg19: chr15-34871296;