chr2-38753089-T-C

Variant names:

• chr2-38753089-T-C
• rs13024811
• ENST00000409011.5:c.-281+1271T>C

Variant summary

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

The ENST00000409011.5(GEMIN6):​c.-281+1271T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,910 control chromosomes in the GnomAD database, including 38,439 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 0.71 (38439 hom., cov: 31)
• Consequence: GEMIN6 ENST00000409011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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+1271T>C		intron_variant	Intron 1 of 5	1		ENSP00000387191.1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107720 AN: 151790 Hom.: 38424 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.709 AC: 107777 AN: 151910 Hom.: 38439 Cov.: 31 AF XY: 0.712 AC XY: 52828 AN XY: 74234

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.734

Alfa AF: 0.700 Hom.: 43616

Bravo AF: 0.710

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13024811; hg19: chr2-38980231;