ENST00000409011.5:c.-280-7630C>T

Variant names:

• chr2-38760475-C-T
• rs6715866
• ENST00000409011.5:c.-280-7630C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.95).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GEMIN6	ENST00000409011.5	c.-280-7630C>T		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.342 AC: 14112 AN: 41312

American (AMR) AF: 0.609 AC: 9255 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2254 AN: 3466

East Asian (EAS) AF: 0.861 AC: 4437 AN: 5156

South Asian (SAS) AF: 0.688 AC: 3287 AN: 4776

European-Finnish (FIN) AF: 0.612 AC: 6408 AN: 10470

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42354 AN: 67892

Other (OTH) AF: 0.596 AC: 1259 AN: 2114

Alfa AF: 0.557 Hom.: 3728

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
PhyloP100		0.45
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: rs6715866; hg19: chr2-38987617;