chr15-30562188-C-T

Variant names:

• chr15-30562188-C-T
• rs200069148
• NM_001355476.2:c.1671C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001355476.2(GOLGA8Q):​c.1671C>T​(p.Pro557Pro) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. P557P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 10)
  • Exomes 𝑓: 0.000041 (14 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8Q NM_001355476.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 0 publications found

Genes affected

GOLGA8Q (HGNC:44408): (golgin A8 family member Q) 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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP7: Synonymous conserved (PhyloP=-0.582 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355476.2. 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
	GOLGA8Q	NM_001355476.2	MANE Select	c.1671C>T	p.Pro557Pro	synonymous	Exon 18 of 19	NP_001342405.1	H3BV12

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA8Q	ENST00000562783.2	TSL:5 MANE Select	c.1671C>T	p.Pro557Pro	synonymous	Exon 18 of 19	ENSP00000457904.1	H3BV12
	ARHGAP11B-DT	ENST00000749391.1		n.538-21907G>A		intron	N/A
	ARHGAP11B-DT	ENST00000749392.1		n.677-21907G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000257 AC: 2 AN: 77918 Hom.: 0 Cov.: 10

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000460

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

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000411 AC: 41 AN: 998210 Hom.: 14 Cov.: 29 AF XY: 0.0000525 AC XY: 26 AN XY: 494818

African (AFR) AF: 0.00 AC: 0 AN: 14434

American (AMR) AF: 0.00 AC: 0 AN: 32376

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17934

East Asian (EAS) AF: 0.0000831 AC: 3 AN: 36084

South Asian (SAS) AF: 0.00 AC: 0 AN: 63792

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25458

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2850

European-Non Finnish (NFE) AF: 0.0000485 AC: 37 AN: 763310

Other (OTH) AF: 0.0000238 AC: 1 AN: 41972

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000257 AC: 2 AN: 77918 Hom.: 0 Cov.: 10 AF XY: 0.0000266 AC XY: 1 AN XY: 37616

African (AFR) AF: 0.00 AC: 0 AN: 13134

American (AMR) AF: 0.00 AC: 0 AN: 9066

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2156

East Asian (EAS) AF: 0.000460 AC: 2 AN: 4352

South Asian (SAS) AF: 0.00 AC: 0 AN: 2784

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5204

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 170

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 39512

Other (OTH) AF: 0.00 AC: 0 AN: 1046

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.59
PhyloP100		-0.58

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: rs200069148; hg19: chr15-30854391;