2-38753780-G-A

Variant names:

• chr2-38753780-G-A
• rs2037875
• ENST00000409011.5:c.-281+1962G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409011.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GEMIN6	ENST00000409011.5	TSL:1	c.-281+1962G>A		intron	N/A	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

African (AFR) AF: 0.340 AC: 14083 AN: 41460

American (AMR) AF: 0.606 AC: 9266 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2256 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4493 AN: 5186

South Asian (SAS) AF: 0.682 AC: 3295 AN: 4828

European-Finnish (FIN) AF: 0.612 AC: 6465 AN: 10560

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41889 AN: 67970

Other (OTH) AF: 0.596 AC: 1254 AN: 2104

Alfa AF: 0.586 Hom.: 63774

Bravo AF: 0.538

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.75
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2037875; hg19: chr2-38980922;