chr2-38751622-T-C

Position:

• chr2-38751622-T-C

Variant summary

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

The ENST00000409011(GEMIN6):​c.-477T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 314,408 control chromosomes in the GnomAD database, including 80,447 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 (38491 hom., cov: 29)
  • Exomes 𝑓: 0.71 (41956 hom.)
• Consequence: GEMIN6 ENST00000409011 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38751622T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GEMIN6	ENST00000409011	c.-477T>C		5_prime_UTR_variant	1/6	1		ENSP00000387191.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107705 AN: 151528 Hom.: 38474 Cov.: 29

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.714 AC: 116159 AN: 162762 Hom.: 41956 Cov.: 0 AF XY: 0.715 AC XY: 62165 AN XY: 86914

Gnomad4 AFR exome AF: 0.726

Gnomad4 AMR exome AF: 0.671

Gnomad4 ASJ exome AF: 0.777

Gnomad4 EAS exome AF: 0.888

Gnomad4 SAS exome AF: 0.732

Gnomad4 FIN exome AF: 0.678

Gnomad4 NFE exome AF: 0.695

Gnomad4 OTH exome AF: 0.721

GnomAD4 genome AF: 0.711 AC: 107768 AN: 151646 Hom.: 38491 Cov.: 29 AF XY: 0.713 AC XY: 52782 AN XY: 74070

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.734

Alfa AF: 0.695 Hom.: 4724

Bravo AF: 0.711

Asia WGS AF: 0.820 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12621103; hg19: chr2-38978764;