10-97860370-T-C

Variant names:

• chr10-97860370-T-C
• rs1417000
• NM_001010917.3:c.138+787T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010917.3(GOLGA7B):​c.138+787T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,028 control chromosomes in the GnomAD database, including 20,798 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 0.52 (20798 hom., cov: 32)
• Consequence: GOLGA7B NM_001010917.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 1 publications found

Genes affected

GOLGA7B (HGNC:31668): (golgin A7 family member B) Enables enzyme binding activity. Predicted to be involved in peptidyl-L-cysteine S-palmitoylation and protein targeting to membrane. Predicted to be located in Golgi membrane. Predicted to be part of palmitoyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010917.3. 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
	GOLGA7B	NM_001010917.3	MANE Select	c.138+787T>C		intron	N/A	NP_001010917.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA7B	ENST00000370602.6	TSL:1 MANE Select	c.138+787T>C		intron	N/A	ENSP00000359634.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79225 AN: 150922 Hom.: 20803 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.629

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.525 AC: 79236 AN: 151028 Hom.: 20798 Cov.: 32 AF XY: 0.524 AC XY: 38686 AN XY: 73760

African (AFR) AF: 0.456 AC: 18781 AN: 41168

American (AMR) AF: 0.549 AC: 8350 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2187 AN: 3452

East Asian (EAS) AF: 0.689 AC: 3548 AN: 5146

South Asian (SAS) AF: 0.592 AC: 2835 AN: 4790

European-Finnish (FIN) AF: 0.501 AC: 5193 AN: 10372

Middle Eastern (MID) AF: 0.628 AC: 181 AN: 288

European-Non Finnish (NFE) AF: 0.541 AC: 36558 AN: 67608

Other (OTH) AF: 0.561 AC: 1178 AN: 2098

Alfa AF: 0.516 Hom.: 2372

Bravo AF: 0.528

Asia WGS AF: 0.589 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.79
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1417000; hg19: chr10-99620127;