15-30606129-C-T

Variant names:

• chr15-30606129-C-T
• rs143536437
• NM_001282490.2:c.168+167C>T

Variant summary

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

The NM_001282490.2(GOLGA8H):​c.168+167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,330 control chromosomes in the GnomAD database, including 4,595 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 0.22 (4595 hom., cov: 30)
• Consequence: GOLGA8H NM_001282490.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 5 publications found

Genes affected

GOLGA8H (HGNC:37443): (golgin A8 family member H) 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]

ARHGAP11B-DT (HGNC:55586): (ARHGAP11B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8H	NM_001282490.2	c.168+167C>T		intron_variant	Intron 2 of 18	ENST00000566740.2	NP_001269419.1
ARHGAP11B-DT	NR_157593.1	n.851-11837G>A		intron_variant	Intron 1 of 1
ARHGAP11B-DT	NR_157594.1	n.849+2089G>A		intron_variant	Intron 4 of 4
ARHGAP11B-DT	NR_157595.1	n.513-11837G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8H	ENST00000566740.2	c.168+167C>T		intron_variant	Intron 2 of 18	5	NM_001282490.2	ENSP00000456894.1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33882 AN: 151214 Hom.: 4596 Cov.: 30

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.224 AC: 33895 AN: 151330 Hom.: 4595 Cov.: 30 AF XY: 0.222 AC XY: 16398 AN XY: 73940

African (AFR) AF: 0.174 AC: 7136 AN: 41008

American (AMR) AF: 0.171 AC: 2606 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3466

East Asian (EAS) AF: 0.0115 AC: 59 AN: 5116

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10530

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18561 AN: 67854

Other (OTH) AF: 0.215 AC: 452 AN: 2098

Alfa AF: 0.126 Hom.: 231

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.36
DANN	Benign	0.74
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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: rs143536437; hg19: chr15-30898332;