15-34531704-A-G

Variant names:

• chr15-34531704-A-G
• rs529998483
• NM_001023567.5:c.325-9T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_001023567.5(GOLGA8B):​c.325-9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (216 hom., cov: 12)
  • Exomes 𝑓: 0.029 (3057 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8B NM_001023567.5 intron
• Scores: Splicing: ADA: 0.00002340
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.105
• Publications: 0 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=-0.94).
• BP6: Variant 15-34531704-A-G is Benign according to our data. Variant chr15-34531704-A-G is described in ClinVar as Benign. ClinVar VariationId is 774220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001023567.5. 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
	GOLGA8B	NM_001023567.5	MANE Select	c.325-9T>C		intron	N/A	NP_001018861.3	A8MQT2-1
	GOLGA8B	NR_027410.2		n.2763-9T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA8B	ENST00000683415.1	MANE Select	c.325-9T>C		intron	N/A	ENSP00000507830.1	A8MQT2-1
	GOLGA8B	ENST00000342314.9	TSL:1	c.325-9T>C		intron	N/A	ENSP00000343064.5	A8MQT2-1
	GOLGA8B	ENST00000484716.5	TSL:1	n.2649-9T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0178 AC: 1553 AN: 87352 Hom.: 216 Cov.: 12

Gnomad AFR AF: 0.00474

Gnomad AMI AF: 0.0248

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00529

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0153

GnomAD2 exomes AF: 0.0240 AC: 1228 AN: 51098 AF XY: 0.0228

Gnomad AFR exome AF: 0.00537

Gnomad AMR exome AF: 0.0169

Gnomad ASJ exome AF: 0.0497

Gnomad EAS exome AF: 0.000443

Gnomad FIN exome AF: 0.00352

Gnomad NFE exome AF: 0.0392

Gnomad OTH exome AF: 0.0240

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0289 AC: 11003 AN: 381382 Hom.: 3057 Cov.: 0 AF XY: 0.0284 AC XY: 5825 AN XY: 205432

African (AFR) AF: 0.00645 AC: 88 AN: 13640

American (AMR) AF: 0.0174 AC: 348 AN: 19964

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 847 AN: 14858

East Asian (EAS) AF: 0.000362 AC: 6 AN: 16564

South Asian (SAS) AF: 0.0124 AC: 510 AN: 40970

European-Finnish (FIN) AF: 0.00372 AC: 93 AN: 24968

Middle Eastern (MID) AF: 0.0496 AC: 83 AN: 1674

European-Non Finnish (NFE) AF: 0.0369 AC: 8360 AN: 226856

Other (OTH) AF: 0.0305 AC: 668 AN: 21888

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0178 AC: 1554 AN: 87442 Hom.: 216 Cov.: 12 AF XY: 0.0168 AC XY: 697 AN XY: 41424

African (AFR) AF: 0.00473 AC: 149 AN: 31526

American (AMR) AF: 0.0189 AC: 152 AN: 8042

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 131 AN: 2258

East Asian (EAS) AF: 0.00 AC: 0 AN: 1518

South Asian (SAS) AF: 0.00587 AC: 10 AN: 1704

European-Finnish (FIN) AF: 0.00211 AC: 10 AN: 4732

Middle Eastern (MID) AF: 0.0423 AC: 6 AN: 142

European-Non Finnish (NFE) AF: 0.0297 AC: 1068 AN: 35956

Other (OTH) AF: 0.0152 AC: 17 AN: 1120

Alfa AF: 0.0214 Hom.: 55

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.25
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000023
dbscSNV1_RF	Benign	0.0020
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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: rs529998483; hg19: chr15-34823905;