rs10155047

Variant names:

• chr3-114054105-C-T
• rs10155047
• NM_020817.2:c.91-470G>A

Variant summary

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

The NM_020817.2(CCDC191):​c.91-470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,378 control chromosomes in the GnomAD database, including 1,026 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 0.11 (1024 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2 hom.)
• Consequence: CCDC191 NM_020817.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 1 publications found

Genes affected

CCDC191 (HGNC:29272): (coiled-coil domain containing 191)

QTRT2 (HGNC:25771): (queuine tRNA-ribosyltransferase accessory subunit 2) This gene encodes a subunit of tRNA-guanine transglycosylase. tRNA-guanine transglycosylase is a heterodimeric enzyme complex that plays a critical role in tRNA modification by synthesizing the 7-deazaguanosine queuosine, which is found in tRNAs that code for asparagine, aspartic acid, histidine, and tyrosine. The encoded protein may play a role in the queuosine 5'-monophosphate salvage pathway. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020817.2. 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
	CCDC191	NM_020817.2	MANE Select	c.91-470G>A		intron	N/A	NP_065868.1
	CCDC191	NM_001353766.3		c.90+2272G>A		intron	N/A	NP_001340695.1
	CCDC191	NM_001353767.2		c.205+2272G>A		intron	N/A	NP_001340696.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC191	ENST00000295878.8	TSL:1 MANE Select	c.91-470G>A		intron	N/A	ENSP00000295878.3
	CCDC191	ENST00000480588.1	TSL:5	n.224G>A		splice_region non_coding_transcript_exon	Exon 2 of 5
	CCDC191	ENST00000491000.5	TSL:5	c.90+2272G>A		intron	N/A	ENSP00000418099.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16408 AN: 151998 Hom.: 1018 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.103 AC: 27 AN: 262 Hom.: 2 Cov.: 0 AF XY: 0.0970 AC XY: 13 AN XY: 134

African (AFR) AF: 0.143 AC: 2 AN: 14

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 1 AN: 14

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0891 AC: 18 AN: 202

Other (OTH) AF: 0.286 AC: 4 AN: 14

GnomAD4 genome AF: 0.108 AC: 16450 AN: 152116 Hom.: 1024 Cov.: 32 AF XY: 0.107 AC XY: 7992 AN XY: 74360

African (AFR) AF: 0.161 AC: 6679 AN: 41456

American (AMR) AF: 0.0730 AC: 1116 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.148 AC: 766 AN: 5178

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4822

European-Finnish (FIN) AF: 0.0661 AC: 700 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5997 AN: 67996

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.100 Hom.: 528

Bravo AF: 0.113

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10155047; hg19: chr3-113772952;