rs2037875

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-38753780-G-A
• chr2-38753780-G-C

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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GEMIN6	ENST00000409011.5	c.-281+1962G>A		intron_variant	Intron 1 of 5	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;