Genetic Variant CTD-2194D22.4:n.38+334C>T (chr5-1887703-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000514569.1(CTD-2194D22.4):n.38+334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,060 control chromosomes in the GnomAD database, including 2,636 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 0.18 ( 2636 hom., cov: 32)

Consequence

CTD-2194D22.4
ENST00000514569.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.247

Publications

3 publications found

Variant links:

Genes affected

CTD-2194D22.4 (HGNC:):

CTD-2194D22.4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTD-2194D22.4	NR_109912.1 link	n.39+334C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1 link	n.38+334C>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27871

AN:

151942

Hom.:

2637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.0967

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.183

AC:

27883

AN:

152060

Hom.:

2636

Cov.:

AF XY:

0.183

AC XY:

13643

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.166

AC:

6878

AN:

41516

American (AMR)

AF:

0.144

AC:

2196

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

837

AN:

3464

East Asian (EAS)

AF:

0.109

AC:

564

AN:

5152

South Asian (SAS)

AF:

0.163

AC:

785

AN:

4820

European-Finnish (FIN)

AF:

0.224

AC:

2377

AN:

10596

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13761

AN:

67908

Other (OTH)

AF:

0.163

AC:

343

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1167

2334

3502

4669

5836

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.195

Hom.:

4191

Bravo

AF:

0.176

Asia WGS

AF:

0.142

AC:

496

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

2.8

(source)

DANN

Benign

0.57

PhyloP100

-0.25

PromoterAI

-0.024

Neutral

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over