15-28843203-T-C

Variant names:

• chr15-28843203-T-C
• rs55909016
• NM_001365371.2:c.901A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001365371.2(GOLGA6L7):​c.901A>G​(p.Lys301Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000549 in 429,756 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (3 hom., cov: 34)
  • Exomes 𝑓: 0.00017 (1 hom.)
• Consequence: GOLGA6L7 NM_001365371.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.04

Genes affected

GOLGA6L7 (HGNC:37442): (golgin A6 family like 7) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000291258 (HGNC:):

PDCD6IPP2 (HGNC:49873): (PDCD6IP pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.02998504).
• BP6: Variant 15-28843203-T-C is Benign according to our data. Variant chr15-28843203-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3770832.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L7	NM_001365371.2	c.901A>G	p.Lys301Glu	missense_variant	Exon 9 of 9	ENST00000567390.7	NP_001352300.1
PDCD6IPP2	NR_037599.1	n.1561-3536T>C		intron_variant	Intron 12 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L7	ENST00000567390.7	c.901A>G	p.Lys301Glu	missense_variant	Exon 9 of 9	5	NM_001365371.2	ENSP00000490318.1
ENSG00000291258	ENST00000564604.5	n.369-3536T>C		intron_variant	Intron 3 of 4	4
ENSG00000291258	ENST00000566178.6	n.411-3536T>C		intron_variant	Intron 3 of 4	5
ENSG00000291258	ENST00000700878.1	n.286-3536T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00154 AC: 184 AN: 119818 Hom.: 3 Cov.: 34

Gnomad AFR AF: 0.00530

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000576

Gnomad FIN AF: 0.000115

Gnomad MID AF: 0.00481

Gnomad NFE AF: 0.000205

Gnomad OTH AF: 0.00303

GnomAD4 exome AF: 0.000168 AC: 52 AN: 309858 Hom.: 1 Cov.: 5 AF XY: 0.000145 AC XY: 23 AN XY: 159128

Gnomad4 AFR exome AF: 0.00432

Gnomad4 AMR exome AF: 0.000236

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000442

Gnomad4 SAS exome AF: 0.0000722

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000536

Gnomad4 OTH exome AF: 0.000376

GnomAD4 genome AF: 0.00153 AC: 184 AN: 119898 Hom.: 3 Cov.: 34 AF XY: 0.00152 AC XY: 89 AN XY: 58566

Gnomad4 AFR AF: 0.00529

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000576

Gnomad4 FIN AF: 0.000115

Gnomad4 NFE AF: 0.000205

Gnomad4 OTH AF: 0.00300

Alfa AF: 0.0239 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA6L7: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.57
DANN	Benign	0.22
FATHMM_MKL	Benign	0.011	N
LIST_S2	Benign	0.62	T
MetaRNN	Benign	0.030	T
GERP RS		0.43
Varity_R		0.050
gMVP		0.0045

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55909016; hg19: chr15-29088349;