2-38753780-G-A

Position:

• chr2-38753780-G-A

Variant summary

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

The ENST00000409011.5(GEMIN6):​c.-281+1962G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,062 control chromosomes in the GnomAD database, including 24,740 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 0.55 (24740 hom., cov: 33)
• Consequence: GEMIN6 ENST00000409011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

Genes affected

GEMIN6 (HGNC:20044): (gem nuclear organelle associated protein 6) GEMIN6 is part of a large macromolecular complex, localized to both the cytoplasm and the nucleus, that plays a role in the cytoplasmic assembly of small nuclear ribonucleoproteins (snRNPs). Other members of this complex include SMN (MIM 600354), GEMIN2 (SIP1; MIM 602595), GEMIN3 (DDX20; MIM 606168), GEMIN4 (MIM 606969), and GEMIN5 (MIM 607005).[supplied by OMIM, Jul 2002]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38753780G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GEMIN6	ENST00000409011.5	c.-281+1962G>A		intron_variant		1		ENSP00000387191.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83790 AN: 151944 Hom.: 24733 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.551 AC: 83821 AN: 152062 Hom.: 24740 Cov.: 33 AF XY: 0.558 AC XY: 41485 AN XY: 74336

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.596

Alfa AF: 0.604 Hom.: 35602

Bravo AF: 0.538

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037875; hg19: chr2-38980922;