rs759803336

Variant names:

• chr15-22465901-T-A
• rs759803336
• NM_001396956.1:c.1641T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-22465901-T-A
• chr15-22465901-T-C
• chr15-22465901-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001396956.1(GOLGA6L22):​c.1641T>A​(p.His547Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/8 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. H547H) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 5)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L22 NM_001396956.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 0 publications found

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

ENSG00000310081 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.06746134).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396956.1. 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
	GOLGA6L22	NM_001396956.1	MANE Select	c.1641T>A	p.His547Gln	missense	Exon 8 of 9	NP_001383885.1	H0YM25
	GOLGA6L22	NM_001396957.1		c.1638T>A	p.His546Gln	missense	Exon 8 of 9	NP_001383886.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L22	ENST00000622895.2	TSL:5 MANE Select	c.1641T>A	p.His547Gln	missense	Exon 8 of 9	ENSP00000483673.2	H0YM25
	ENSG00000310081	ENST00000846990.1		n.151+4510A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 43084 Hom.: 0 Cov.: 5

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: 1039812 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 519176

African (AFR) AF: 0.00 AC: 0 AN: 15160

American (AMR) AF: 0.00 AC: 0 AN: 28404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17418

East Asian (EAS) AF: 0.00 AC: 0 AN: 23764

South Asian (SAS) AF: 0.00 AC: 0 AN: 64204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41652

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2566

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 806012

Other (OTH) AF: 0.00 AC: 0 AN: 40632

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 43084 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 20442

African (AFR) AF: 0.00 AC: 0 AN: 6794

American (AMR) AF: 0.00 AC: 0 AN: 3424

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1256

East Asian (EAS) AF: 0.00 AC: 0 AN: 1574

South Asian (SAS) AF: 0.00 AC: 0 AN: 1084

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2300

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 32

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 25854

Other (OTH) AF: 0.00 AC: 0 AN: 560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.051
DANN	Benign	0.26
LIST_S2	Benign	0.086	T
MetaRNN	Benign	0.067	T
PhyloP100		-0.035
Sift4G	Benign	0.47	T
Vest4		0.13
gMVP		0.011

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: rs759803336; hg19: chr15-23407195;