2-38760475-C-T

Position:

• chr2-38760475-C-T

Variant summary

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

The ENST00000409011.5(GEMIN6):​c.-280-7630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,590 control chromosomes in the GnomAD database, including 25,008 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 0.56 (25008 hom., cov: 30)
• Consequence: GEMIN6 ENST00000409011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38760475C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GEMIN6	ENST00000409011.5	c.-280-7630C>T		intron_variant		1		ENSP00000387191.1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84159 AN: 151470 Hom.: 25001 Cov.: 30

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.555 AC: 84191 AN: 151590 Hom.: 25008 Cov.: 30 AF XY: 0.562 AC XY: 41606 AN XY: 74048

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.596

Alfa AF: 0.565 Hom.: 3687

Bravo AF: 0.542

Asia WGS AF: 0.757 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6715866; hg19: chr2-38987617;