15-23129937-C-A

Variant names:

• chr15-23129937-C-A
• rs774621315
• NM_001001413.3:c.1516G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001001413.3(GOLGA6L1):​c.1516G>T​(p.Asp506Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D506N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 20)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L1 NM_001001413.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.08
• Publications: 0 publications found

Genes affected

GOLGA6L1 (HGNC:37444): (golgin A6 family like 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.13942817).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001413.3. 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
	GOLGA6L1	NM_001001413.3	MANE Select	c.1516G>T	p.Asp506Tyr	missense	Exon 8 of 9	NP_001001413.3	Q8N7Z2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L1	ENST00000614055.2	TSL:5 MANE Select	c.1516G>T	p.Asp506Tyr	missense	Exon 8 of 9	ENSP00000478478.1	Q8N7Z2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 115598 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

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: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 553820 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 294712

African (AFR) AF: 0.00 AC: 0 AN: 15902

American (AMR) AF: 0.00 AC: 0 AN: 27650

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17284

East Asian (EAS) AF: 0.00 AC: 0 AN: 28064

South Asian (SAS) AF: 0.00 AC: 0 AN: 55050

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2382

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 344242

Other (OTH) AF: 0.00 AC: 0 AN: 28022

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 115680 Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0 AN XY: 55650

African (AFR) AF: 0.00 AC: 0 AN: 31744

American (AMR) AF: 0.00 AC: 0 AN: 11548

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2926

East Asian (EAS) AF: 0.00 AC: 0 AN: 3118

South Asian (SAS) AF: 0.00 AC: 0 AN: 2814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6930

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 138

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 54220

Other (OTH) AF: 0.00 AC: 0 AN: 1568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.35
FATHMM_MKL	Benign	0.0030	N
LIST_S2	Benign	0.70	T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.14	T
PhyloP100		-4.1
Sift4G	Uncertain	0.010	D
Vest4		0.24
MVP		0.27
GERP RS		0.15
Varity_R		0.050
gMVP		0.017

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: rs774621315; hg19: chr15-23407377;