Genetic Variant ENSG00000258744:n.*61G>A (chr14-24508761-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 ENST00000555109.2(ENSG00000258744):n.*61G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,970 control chromosomes in the GnomAD database, including 7,373 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 ( 7370 hom., cov: 32)

Exomes 𝑓: 0.31 ( 3 hom. )

Consequence

ENSG00000258744
ENST00000555109.2 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.643

Publications

4 publications found

Variant links:

Genes affected

ENSG00000258744 (HGNC:):

ENSG00000258744 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258744	ENST00000555109.2 link	n.*61G>A		downstream_gene_variant		5
ENSG00000258744	ENST00000816252.1 link	n.*61G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45716

AN:

151804

Hom.:

7357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.313

AC:

AN:

Hom.:

AF XY:

0.269

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.262

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.301

AC:

45764

AN:

151922

Hom.:

7370

Cov.:

AF XY:

0.311

AC XY:

23078

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.270

AC:

11206

AN:

41428

American (AMR)

AF:

0.471

AC:

7186

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1131

AN:

3468

East Asian (EAS)

AF:

0.415

AC:

2148

AN:

5178

South Asian (SAS)

AF:

0.323

AC:

1554

AN:

4814

European-Finnish (FIN)

AF:

0.346

AC:

3640

AN:

10512

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17807

AN:

67942

Other (OTH)

AF:

0.318

AC:

670

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1581

3161

4742

6322

7903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.270

Hom.:

1374

Bravo

AF:

0.313

Asia WGS

AF:

0.380

AC:

1323

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.9

(source)

DANN

Benign

0.80

PhyloP100

-0.64

PromoterAI

-0.050

Neutral

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over