rs2129571

Variant names:

• chr3-114034724-G-A
• rs2129571
• NM_020817.2:c.818+201C>T

Variant summary

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

The NM_020817.2(CCDC191):​c.818+201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,158 control chromosomes in the GnomAD database, including 912 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 0.10 (912 hom., cov: 32)
• Consequence: CCDC191 NM_020817.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC191	NM_020817.2	c.818+201C>T		intron_variant	Intron 6 of 16	ENST00000295878.8	NP_065868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC191	ENST00000295878.8	c.818+201C>T		intron_variant	Intron 6 of 16	1	NM_020817.2	ENSP00000295878.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15740 AN: 152040 Hom.: 908 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.104 AC: 15781 AN: 152158 Hom.: 912 Cov.: 32 AF XY: 0.103 AC XY: 7668 AN XY: 74394

African (AFR) AF: 0.147 AC: 6086 AN: 41498

American (AMR) AF: 0.0722 AC: 1104 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.148 AC: 763 AN: 5168

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.0658 AC: 697 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0875 AC: 5950 AN: 68004

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0940 Hom.: 1043

Bravo AF: 0.108

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.18
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2129571; hg19: chr3-113753571;