Genetic Variant ENSG00000287146:n.363-5109C>T (chr22-19323289-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 ENST00000664918.1(ENSG00000287146):n.363-5109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,008 control chromosomes in the GnomAD database, including 8,014 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 0.32 ( 8014 hom., cov: 32)

Consequence

ENSG00000287146
ENST00000664918.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.184

Publications

4 publications found

Variant links:

Genes affected

ENSG00000287146 (HGNC:):

ENSG00000287146 links:

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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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105372859	XR_938000.3 link	n.385-5109C>T	intron_variant	Intron 1 of 4
LOC105372859	XR_938001.3 link	n.385-5109C>T	intron_variant	Intron 1 of 4
LOC105372859	XR_938002.3 link	n.385-5109C>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287146	ENST00000664918.1 link	n.363-5109C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48233

AN:

151890

Hom.:

8016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.309

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

GnomAD4 genome

AF:

0.317

AC:

48236

AN:

152008

Hom.:

8014

Cov.:

AF XY:

0.318

AC XY:

23639

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.222

AC:

9197

AN:

41462

American (AMR)

AF:

0.300

AC:

4577

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

1001

AN:

3472

East Asian (EAS)

AF:

0.428

AC:

2217

AN:

5174

South Asian (SAS)

AF:

0.239

AC:

1151

AN:

4824

European-Finnish (FIN)

AF:

0.411

AC:

4341

AN:

10552

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.363

AC:

24659

AN:

67934

Other (OTH)

AF:

0.304

AC:

643

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1672

3344

5015

6687

8359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.348

Hom.:

37894

Bravo

AF:

0.310

Asia WGS

AF:

0.295

AC:

1025

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.9

(source)

DANN

Benign

0.89

PhyloP100

0.18

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