dbSNP rs12655062: CTD-2194D22.4:n.108+2481G>A (chr5-1890763-G-A) – 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.108+2481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,140 control chromosomes in the GnomAD database, including 7,835 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 0.30 ( 7835 hom., cov: 33)

Consequence

CTD-2194D22.4
ENST00000514569.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Publications

4 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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.109+2481G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1 link	n.108+2481G>A		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46250

AN:

152022

Hom.:

7825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.423

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.338

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

GnomAD4 genome

AF:

0.304

AC:

46280

AN:

152140

Hom.:

7835

Cov.:

AF XY:

0.314

AC XY:

23340

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.155

AC:

6428

AN:

41498

American (AMR)

AF:

0.410

AC:

6268

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1333

AN:

3472

East Asian (EAS)

AF:

0.342

AC:

1769

AN:

5178

South Asian (SAS)

AF:

0.362

AC:

1747

AN:

4824

European-Finnish (FIN)

AF:

0.423

AC:

4478

AN:

10578

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.341

AC:

23181

AN:

67980

Other (OTH)

AF:

0.342

AC:

724

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1603

3206

4809

6412

8015

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.318

Hom.:

16050

Bravo

AF:

0.296

Asia WGS

AF:

0.364

AC:

1266

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.74

PhyloP100

-0.22

Splicing

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

Publications

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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