chr2-38754065-G-A

Variant names:

• chr2-38754065-G-A
• rs10197412
• ENST00000409011.5:c.-281+2247G>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+2247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,052 control chromosomes in the GnomAD database, including 24,874 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 (24874 hom., cov: 33)
• Consequence: GEMIN6 ENST00000409011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GEMIN6	ENST00000409011.5	TSL:1	c.-281+2247G>A		intron	N/A	ENSP00000387191.1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83974 AN: 151934 Hom.: 24868 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.552 AC: 84004 AN: 152052 Hom.: 24874 Cov.: 33 AF XY: 0.560 AC XY: 41593 AN XY: 74330

African (AFR) AF: 0.340 AC: 14076 AN: 41450

American (AMR) AF: 0.609 AC: 9320 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4513 AN: 5178

South Asian (SAS) AF: 0.686 AC: 3315 AN: 4830

European-Finnish (FIN) AF: 0.611 AC: 6459 AN: 10564

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41973 AN: 67952

Other (OTH) AF: 0.598 AC: 1264 AN: 2112

Alfa AF: 0.561 Hom.: 3624

Bravo AF: 0.539

Asia WGS AF: 0.765 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.28
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: rs10197412; hg19: chr2-38981207;