rs11337

chr8-41510767-T-G

Variant summary

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

The NM_001002296.2(GOLGA7):c.*1199T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,784 control chromosomes in the GnomAD database, including 65,637 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 0.93 (65386 hom., cov: 32)
  • Exomes 𝑓: 0.95 (251 hom.)
• Consequence: GOLGA7 NM_001002296.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.53

Genes affected

GOLGA7 (HGNC:24876): (golgin A7) Involved in Golgi to plasma membrane protein transport; peptidyl-L-cysteine S-palmitoylation; and protein stabilization. Acts upstream of or within Golgi to plasma membrane transport. Located in Golgi membrane and Golgi stack. Is intrinsic component of Golgi membrane. Part of palmitoyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

GPAT4-AS1 (HGNC:55539): (GPAT4 and GINS4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA7	NM_001002296.2	c.*1199T>G		3_prime_UTR_variant	5/5	ENST00000357743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA7	ENST00000357743.9	c.*1199T>G		3_prime_UTR_variant	5/5	1	NM_001002296.2	P1
GPAT4-AS1	ENST00000523081.2	n.2859A>C		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140795 AN: 152112 Hom.: 65343 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.928

GnomAD4 exome AF: 0.953 AC: 528 AN: 554 Hom.: 251 Cov.: 0 AF XY: 0.949 AC XY: 336 AN XY: 354

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.875

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.946

Gnomad4 NFE exome AF: 0.979

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.926 AC: 140896 AN: 152230 Hom.: 65386 Cov.: 32 AF XY: 0.923 AC XY: 68713 AN XY: 74432

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.940

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.927

Alfa AF: 0.941 Hom.: 27095

Bravo AF: 0.921

Asia WGS AF: 0.868 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	12
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11337; hg19: chr8-41368286;