rs2867301

Positions:

• chr1-150681319-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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]

ACMG classification

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
GOLPH3L	NM_018178.6	c.183+13337G>A		intron_variant		ENST00000271732.8
GOLPH3L	XM_006711428.3	c.225+13337G>A		intron_variant
GOLPH3L	XM_047424285.1	c.225+13337G>A		intron_variant
GOLPH3L	XM_047424286.1	c.225+13337G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLPH3L	ENST00000271732.8	c.183+13337G>A		intron_variant		1	NM_018178.6	P1
GOLPH3L	ENST00000427665.1	c.249+12789G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58515 AN: 151734 Hom.: 11595 Cov.: 31

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

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

Other links and lift over

dbSNP: rs2867301; hg19: chr1-150653795;