rs910924

Variant names:

• chr17-752680-G-A
• rs910924
• ENST00000449830.6:n.14G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449830.6(DBIL5P):​n.14G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 981,524 control chromosomes in the GnomAD database, including 32,060 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 0.20 (3567 hom., cov: 33)
  • Exomes 𝑓: 0.26 (28493 hom.)
• Consequence: DBIL5P ENST00000449830.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 42 publications found

Genes affected

DBIL5P (HGNC:):

DBIL5P (HGNC:38519): (diazepam binding inhibitor-like 5, pseudogene)

GEMIN4 (HGNC:15717): (gem nuclear organelle associated protein 4) The product of this gene is part of a large complex localized to the cytoplasm, nucleoli, and to discrete nuclear bodies called Gemini bodies (gems). The complex functions in spliceosomal snRNP assembly in the cytoplasm, and regenerates spliceosomes required for pre-mRNA splicing in the nucleus. The encoded protein directly interacts with a DEAD box protein and several spliceosome core proteins. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GEMIN4 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalities

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449830.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBIL5P	NR_024120.2		n.348G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBIL5P	ENST00000449830.6	TSL:2	n.14G>A		non_coding_transcript_exon	Exon 1 of 2
	DBIL5P	ENST00000536214.2	TSL:6	n.69G>A		non_coding_transcript_exon	Exon 1 of 1
	GEMIN4	ENST00000570364.5	TSL:3	c.-137C>T		5_prime_UTR	Exon 1 of 3	ENSP00000461103.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30209 AN: 152070 Hom.: 3565 Cov.: 33

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.257 AC: 213018 AN: 829336 Hom.: 28493 Cov.: 14 AF XY: 0.256 AC XY: 98662 AN XY: 384974

African (AFR) AF: 0.0768 AC: 1253 AN: 16324

American (AMR) AF: 0.153 AC: 236 AN: 1538

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 1384 AN: 5840

East Asian (EAS) AF: 0.118 AC: 653 AN: 5542

South Asian (SAS) AF: 0.186 AC: 3009 AN: 16206

European-Finnish (FIN) AF: 0.189 AC: 530 AN: 2810

Middle Eastern (MID) AF: 0.149 AC: 259 AN: 1736

European-Non Finnish (NFE) AF: 0.265 AC: 198920 AN: 751452

Other (OTH) AF: 0.243 AC: 6774 AN: 27888

GnomAD4 genome AF: 0.199 AC: 30215 AN: 152188 Hom.: 3567 Cov.: 33 AF XY: 0.196 AC XY: 14563 AN XY: 74384

African (AFR) AF: 0.0923 AC: 3836 AN: 41556

American (AMR) AF: 0.164 AC: 2501 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3470

East Asian (EAS) AF: 0.119 AC: 616 AN: 5162

South Asian (SAS) AF: 0.218 AC: 1047 AN: 4812

European-Finnish (FIN) AF: 0.195 AC: 2061 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18401 AN: 67996

Other (OTH) AF: 0.215 AC: 453 AN: 2108

Alfa AF: 0.249 Hom.: 9785

Bravo AF: 0.192

Asia WGS AF: 0.189 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.3
DANN	Benign	0.92
PhyloP100		-0.24
PromoterAI		-0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs910924; hg19: chr17-655920; COSMIC: COSV107394942;