rs143536437

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-30606129-C-G
• chr15-30606129-C-T

Variant summary

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

The NM_001282490.2(GOLGA8H):​c.168+167C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000926 in 151,268 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000093 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8H	NM_001282490.2	c.168+167C>G		intron_variant	Intron 2 of 18	ENST00000566740.2	NP_001269419.1
ARHGAP11B-DT	NR_157593.1	n.851-11837G>C		intron_variant	Intron 1 of 1
ARHGAP11B-DT	NR_157594.1	n.849+2089G>C		intron_variant	Intron 4 of 4
ARHGAP11B-DT	NR_157595.1	n.513-11837G>C		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>G		intron_variant	Intron 2 of 18	5	NM_001282490.2	ENSP00000456894.1

Frequencies

GnomAD3 genomes AF: 0.0000926 AC: 14 AN: 151268 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000734

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000591

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: 0.0000147

Gnomad OTH AF: 0.000481

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

GnomAD4 genome AF: 0.0000926 AC: 14 AN: 151268 Hom.: 0 Cov.: 30 AF XY: 0.0000948 AC XY: 7 AN XY: 73848

African (AFR) AF: 0.0000734 AC: 3 AN: 40896

American (AMR) AF: 0.000591 AC: 9 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5128

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67882

Other (OTH) AF: 0.000481 AC: 1 AN: 2078

Alfa AF: 0.00 Hom.: 231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.38
PhyloP100		0.12

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;