rs7057480

Variant names:

• chrX-14026123-G-A
• rs7057480
• NM_001042479.2:c.-34+17C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-14026123-G-A
• chrX-14026123-G-C

Variant summary

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

The NM_001042479.2(GEMIN8):​c.-34+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 744,695 control chromosomes in the GnomAD database, including 23,136 homozygotes. There are 64,827 hemizygotes in GnomAD. 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 0.26 (2747 hom., 8260 hem., cov: 23)
  • Exomes 𝑓: 0.30 (20389 hom. 56567 hem.)
• Consequence: GEMIN8 NM_001042479.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 2 publications found

Genes affected

GEMIN8 (HGNC:26044): (gem nuclear organelle associated protein 8) The protein encoded by this gene is part of the SMN complex, which is necessary for spliceosomal snRNP assembly in the cytoplasm and pre-mRNA splicing in the nucleus. The encoded protein binds to both SMN1 and the GEMIN6/GEMIN7 heterodimer, mediating their interaction. This protein is found in nuclear Gemini of Cajal bodies (gems) and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, May 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GEMIN8	NM_001042479.2	c.-34+17C>T		intron_variant	Intron 2 of 4	ENST00000680255.1	NP_001035944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GEMIN8	ENST00000680255.1	c.-34+17C>T		intron_variant	Intron 2 of 4		NM_001042479.2	ENSP00000505429.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 28398 AN: 111123 Hom.: 2747 Cov.: 23

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.301 AC: 190816 AN: 633519 Hom.: 20389 Cov.: 13 AF XY: 0.305 AC XY: 56567 AN XY: 185643

African (AFR) AF: 0.206 AC: 2525 AN: 12264

American (AMR) AF: 0.185 AC: 150 AN: 810

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 1020 AN: 3925

East Asian (EAS) AF: 0.0103 AC: 31 AN: 2998

South Asian (SAS) AF: 0.332 AC: 3920 AN: 11822

European-Finnish (FIN) AF: 0.240 AC: 141 AN: 588

Middle Eastern (MID) AF: 0.302 AC: 328 AN: 1087

European-Non Finnish (NFE) AF: 0.305 AC: 176834 AN: 579090

Other (OTH) AF: 0.280 AC: 5867 AN: 20935

GnomAD4 genome AF: 0.255 AC: 28395 AN: 111176 Hom.: 2747 Cov.: 23 AF XY: 0.247 AC XY: 8260 AN XY: 33414

African (AFR) AF: 0.211 AC: 6457 AN: 30592

American (AMR) AF: 0.210 AC: 2213 AN: 10535

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 644 AN: 2626

East Asian (EAS) AF: 0.0112 AC: 40 AN: 3567

South Asian (SAS) AF: 0.306 AC: 809 AN: 2648

European-Finnish (FIN) AF: 0.270 AC: 1591 AN: 5902

Middle Eastern (MID) AF: 0.240 AC: 52 AN: 217

European-Non Finnish (NFE) AF: 0.303 AC: 16031 AN: 52893

Other (OTH) AF: 0.234 AC: 354 AN: 1516

Alfa AF: 0.277 Hom.: 5322

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.57
PhyloP100		0.075
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs7057480; hg19: chrX-14044242;