Genetic Variant ENSG00000295614:n.309-18676C>T (chr18-22564362-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 ENST00000731318.1(ENSG00000295614):n.309-18676C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,954 control chromosomes in the GnomAD database, including 6,318 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 0.28 ( 6318 hom., cov: 32)

Consequence

ENSG00000295614
ENST00000731318.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109

Publications

4 publications found

Variant links:

Genes affected

ENSG00000295614 (HGNC:):

ENSG00000295614 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904265	XR_007066310.1 link	n.196-18676C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000295614	ENST00000731318.1 link	n.309-18676C>T	intron_variant	Intron 2 of 2
ENSG00000295614	ENST00000731322.1 link	n.277-241C>T	intron_variant	Intron 2 of 3
ENSG00000295614	ENST00000731317.1 link	n.*166C>T	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41932

AN:

151836

Hom.:

6311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.297

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

GnomAD4 genome

AF:

0.276

AC:

41960

AN:

151954

Hom.:

6318

Cov.:

AF XY:

0.279

AC XY:

20752

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.176

AC:

7284

AN:

41452

American (AMR)

AF:

0.435

AC:

6643

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

1056

AN:

3468

East Asian (EAS)

AF:

0.191

AC:

984

AN:

5152

South Asian (SAS)

AF:

0.266

AC:

1280

AN:

4812

European-Finnish (FIN)

AF:

0.307

AC:

3230

AN:

10536

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.302

AC:

20517

AN:

67960

Other (OTH)

AF:

0.296

AC:

625

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1488

2976

4463

5951

7439

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.283

Hom.:

787

Bravo

AF:

0.283

Asia WGS

AF:

0.242

AC:

842

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.4

(source)

DANN

Benign

0.75

PhyloP100

0.11

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