Genetic Variant ENST00000584546.5:n.261-59C>T (chr18-27501924-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 ENST00000584546.5(ENSG00000264151):n.261-59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,328 control chromosomes in the GnomAD database, including 482 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 0.071 ( 482 hom., cov: 32)

Exomes 𝑓: 0.050 ( 0 hom. )

Consequence

ENSG00000264151
ENST00000584546.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

2 publications found

Variant links:

Genes affected

ENSG00000264151 (HGNC:):

ENSG00000264151 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 (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985126	XR_001753533.1 link	n.293-59C>T		intron_variant	Intron 3 of 3
LOC107985126	XR_001753535.1 link	n.241-59C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264151	ENST00000584546.5 link	n.261-59C>T		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.0711

AC:

10819

AN:

152170

Hom.:

486

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0834

Gnomad ASJ

AF:

0.0841

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0366

Gnomad FIN

AF:

0.0539

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0526

Gnomad OTH

AF:

0.0871

GnomAD4 exome

AF:

0.0500

AC:

AN:

Hom.:

AF XY:

0.0385

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0909

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.700

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0711

AC:

10833

AN:

152288

Hom.:

482

Cov.:

AF XY:

0.0697

AC XY:

5189

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.113

AC:

4696

AN:

41552

American (AMR)

AF:

0.0835

AC:

1278

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0841

AC:

292

AN:

3470

East Asian (EAS)

AF:

0.000579

AC:

AN:

5180

South Asian (SAS)

AF:

0.0367

AC:

177

AN:

4828

European-Finnish (FIN)

AF:

0.0539

AC:

573

AN:

10624

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0527

AC:

3582

AN:

68018

Other (OTH)

AF:

0.0862

AC:

182

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

517

1033

1550

2066

2583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0627

Hom.:

581

Bravo

AF:

0.0785

Asia WGS

AF:

0.0240

AC:

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

2.1

(source)

DANN

Benign

0.71

PhyloP100

0.36

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