rs11337

Variant names:

• chr8-41510767-T-G
• rs11337
• NM_001002296.2:c.*1199T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002296.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA7	NM_001002296.2	MANE Select	c.*1199T>G		3_prime_UTR	Exon 5 of 5	NP_001002296.1
	GOLGA7	NR_156425.2		n.1706T>G		non_coding_transcript_exon	Exon 6 of 6
	GOLGA7	NR_156426.2		n.1634T>G		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA7	ENST00000357743.9	TSL:1 MANE Select	c.*1199T>G		3_prime_UTR	Exon 5 of 5	ENSP00000350378.4
	GOLGA7	ENST00000405786.3	TSL:1	c.*1213T>G		3_prime_UTR	Exon 6 of 6	ENSP00000386030.2
	GOLGA7	ENST00000694877.1		c.*1213T>G		3_prime_UTR	Exon 6 of 6	ENSP00000511562.1

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.875 AC: 7 AN: 8

South Asian (SAS) AF: 1.00 AC: 4 AN: 4

European-Finnish (FIN) AF: 0.946 AC: 405 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.979 AC: 94 AN: 96

Other (OTH) AF: 1.00 AC: 12 AN: 12

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

African (AFR) AF: 0.887 AC: 36816 AN: 41512

American (AMR) AF: 0.926 AC: 14158 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3428 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4054 AN: 5180

South Asian (SAS) AF: 0.924 AC: 4464 AN: 4830

European-Finnish (FIN) AF: 0.940 AC: 9970 AN: 10612

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.954 AC: 64876 AN: 68014

Other (OTH) AF: 0.927 AC: 1957 AN: 2110

Alfa AF: 0.940 Hom.: 32519

Bravo AF: 0.921

Asia WGS AF: 0.868 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		2.5
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11337; hg19: chr8-41368286;