rs2867301

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018178.6(GOLPH3L):​c.183+13337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,852 control chromosomes in the GnomAD database, including 11,605 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 0.39 ( 11605 hom., cov: 31)

Consequence

GOLPH3L
NM_018178.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.472
Variant links:
Genes affected
GOLPH3L (HGNC:24882): (golgi phosphoprotein 3 like) The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is localized at the Golgi stack and may have a regulatory role in Golgi trafficking. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GOLPH3LNM_018178.6 linkuse as main transcriptc.183+13337G>A intron_variant ENST00000271732.8
GOLPH3LXM_006711428.3 linkuse as main transcriptc.225+13337G>A intron_variant
GOLPH3LXM_047424285.1 linkuse as main transcriptc.225+13337G>A intron_variant
GOLPH3LXM_047424286.1 linkuse as main transcriptc.225+13337G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GOLPH3LENST00000271732.8 linkuse as main transcriptc.183+13337G>A intron_variant 1 NM_018178.6 P1Q9H4A5-1
GOLPH3LENST00000427665.1 linkuse as main transcriptc.249+12789G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.386
AC:
58515
AN:
151734
Hom.:
11595
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.268
Gnomad AMR
AF:
0.435
Gnomad ASJ
AF:
0.496
Gnomad EAS
AF:
0.357
Gnomad SAS
AF:
0.550
Gnomad FIN
AF:
0.402
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.405
Gnomad OTH
AF:
0.393
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.386
AC:
58542
AN:
151852
Hom.:
11605
Cov.:
31
AF XY:
0.390
AC XY:
28942
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.308
Gnomad4 AMR
AF:
0.435
Gnomad4 ASJ
AF:
0.496
Gnomad4 EAS
AF:
0.358
Gnomad4 SAS
AF:
0.550
Gnomad4 FIN
AF:
0.402
Gnomad4 NFE
AF:
0.405
Gnomad4 OTH
AF:
0.396
Alfa
AF:
0.410
Hom.:
5899
Bravo
AF:
0.377
Asia WGS
AF:
0.393
AC:
1368
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
4.1
DANN
Benign
0.68

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2867301; hg19: chr1-150653795; API