Genetic Variant ENSG00000295857:n.*95G>A (chr19-54295903-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 ENST00000733241.1(ENSG00000295857):n.*95G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 331,318 control chromosomes in the GnomAD database, including 806 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 0.061 ( 607 hom., cov: 32)

Exomes 𝑓: 0.023 ( 199 hom. )

Consequence

ENSG00000295857
ENST00000733241.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.932

Publications

2 publications found

Variant links:

Genes affected

ENSG00000295857 (HGNC:):

ENSG00000295857 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=-1.03).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.161 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
ENSG00000295857	ENST00000733241.1 link	n.*95G>A		downstream_gene_variant
ENSG00000295857	ENST00000733242.1 link	n.*95G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0606

AC:

9211

AN:

152008

Hom.:

598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.166

Gnomad ASJ

AF:

0.00835

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.0164

Gnomad FIN

AF:

0.0287

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00969

Gnomad OTH

AF:

0.0642

GnomAD4 exome

AF:

0.0230

AC:

4129

AN:

179192

Hom.:

199

Cov.:

AF XY:

0.0220

AC XY:

2172

AN XY:

98578

show subpopulations

African (AFR)

AF:

0.0968

AC:

427

AN:

4412

American (AMR)

AF:

0.162

AC:

1072

AN:

6618

Ashkenazi Jewish (ASJ)

AF:

0.00753

AC:

AN:

4116

East Asian (EAS)

AF:

0.126

AC:

815

AN:

6462

South Asian (SAS)

AF:

0.0107

AC:

392

AN:

36466

European-Finnish (FIN)

AF:

0.0257

AC:

211

AN:

8220

Middle Eastern (MID)

AF:

0.00940

AC:

AN:

638

European-Non Finnish (NFE)

AF:

0.00896

AC:

929

AN:

103740

Other (OTH)

AF:

0.0289

AC:

246

AN:

8520

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

165

329

494

658

823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

168

224

280

<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:

0.0607

AC:

9236

AN:

152126

Hom.:

607

Cov.:

AF XY:

0.0625

AC XY:

4650

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.116

AC:

4800

AN:

41478

American (AMR)

AF:

0.167

AC:

2545

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00835

AC:

AN:

3472

East Asian (EAS)

AF:

0.132

AC:

682

AN:

5172

South Asian (SAS)

AF:

0.0158

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0287

AC:

304

AN:

10590

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00971

AC:

660

AN:

68002

Other (OTH)

AF:

0.0636

AC:

134

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

404

807

1211

1614

2018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0275

Hom.:

390

Bravo

AF:

0.0729

Asia WGS

AF:

0.0850

AC:

295

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

(source)

DANN

Benign

0.40

PhyloP100

-0.93

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