15-22608940-C-G

Variant names:

• chr15-22608940-C-G
• rs764907606
• ENST00000611635.4:n.1535G>C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000611635.4(GOLGA8IP):​n.1535G>C variant causes a non coding transcript exon 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0066 (9 hom., cov: 15)
  • Exomes 𝑓: 0.0063 (131 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA8IP ENST00000611635.4 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.333

Genes affected

GOLGA8IP (HGNC:26660): (golgin A8 family member I, pseudogene) 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]

LOC101927846 (HGNC:):

RN7SL495P (HGNC:46511): (RNA, 7SL, cytoplasmic 495, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 15-22608940-C-G is Benign according to our data. Variant chr15-22608940-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2644958.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927846	XR_001751437.2	n.186+530C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8IP	ENST00000611635.4	n.1535G>C		non_coding_transcript_exon_variant	Exon 14 of 18	6
RN7SL495P	ENST00000616925.1	n.*201G>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 859 AN: 130086 Hom.: 9 Cov.: 15 FAILED QC

Gnomad AFR AF: 0.00658

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00665

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0123

Gnomad FIN AF: 0.000792

Gnomad MID AF: 0.0169

Gnomad NFE AF: 0.00649

Gnomad OTH AF: 0.0118

GnomAD3 exomes AF: 0.00686 AC: 357 AN: 52008 Hom.: 4 AF XY: 0.00624 AC XY: 164 AN XY: 26290

Gnomad AFR exome AF: 0.00910

Gnomad AMR exome AF: 0.00867

Gnomad ASJ exome AF: 0.0242

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00725

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00676

Gnomad OTH exome AF: 0.00773

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00630 AC: 5207 AN: 825978 Hom.: 131 Cov.: 11 AF XY: 0.00631 AC XY: 2669 AN XY: 422754

Gnomad4 AFR exome AF: 0.00699

Gnomad4 AMR exome AF: 0.00866

Gnomad4 ASJ exome AF: 0.0251

Gnomad4 EAS exome AF: 0.0000309

Gnomad4 SAS exome AF: 0.00798

Gnomad4 FIN exome AF: 0.000900

Gnomad4 NFE exome AF: 0.00591

Gnomad4 OTH exome AF: 0.00896

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00660 AC: 859 AN: 130172 Hom.: 9 Cov.: 15 AF XY: 0.00652 AC XY: 408 AN XY: 62554

Gnomad4 AFR AF: 0.00655

Gnomad4 AMR AF: 0.00664

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.000792

Gnomad4 NFE AF: 0.00649

Gnomad4 OTH AF: 0.0117

Alfa AF: 0.00737 Hom.: 3

Bravo AF: 0.00735

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA8IP: PP2, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764907606; hg19: chr15-23264156;