10-97860370-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA7B	NM_001010917.3	c.138+787T>C		intron_variant	Intron 2 of 4	ENST00000370602.6	NP_001010917.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA7B	ENST00000370602.6	c.138+787T>C		intron_variant	Intron 2 of 4	1	NM_001010917.3	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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.561

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417000; hg19: chr10-99620127;