Genetic Variant ENST00000573698.3:n.-68A>G (chr17-6190631-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000573698.3(ENSG00000262231):n.-68A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,292 control chromosomes in the GnomAD database, including 849 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 0.092 ( 849 hom., cov: 32)

Exomes 𝑓: 0.033 ( 0 hom. )

Consequence

ENSG00000262231
ENST00000573698.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.191

Publications

8 publications found

Variant links:

Genes affected

ENSG00000262231 (HGNC:):

ENSG00000262231 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371508	XR_934184.2 link	n.-84A>G		upstream_gene_variant
LOC105371508	XR_934185.3 link	n.-84A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000262231	ENST00000573698.3 link	n.-68A>G	upstream_gene_variant	2
ENSG00000262231	ENST00000664051.1 link	n.-121A>G	upstream_gene_variant
ENSG00000262231	ENST00000736076.1 link	n.-103A>G	upstream_gene_variant
ENSG00000262231	ENST00000736077.1 link	n.-106A>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14055

AN:

152144

Hom.:

849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.0588

Gnomad FIN

AF:

0.0571

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0523

Gnomad OTH

AF:

0.0826

GnomAD4 exome

AF:

0.0333

AC:

AN:

Hom.:

AF XY:

0.0455

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:

0.00

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:

0.0556

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0925

AC:

14084

AN:

152262

Hom.:

849

Cov.:

AF XY:

0.0922

AC XY:

6866

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.158

AC:

6570

AN:

41548

American (AMR)

AF:

0.104

AC:

1590

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

351

AN:

3470

East Asian (EAS)

AF:

0.182

AC:

940

AN:

5174

South Asian (SAS)

AF:

0.0581

AC:

280

AN:

4822

European-Finnish (FIN)

AF:

0.0571

AC:

606

AN:

10608

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0523

AC:

3558

AN:

68020

Other (OTH)

AF:

0.0822

AC:

174

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

630

1260

1890

2520

3150

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0730

Hom.:

876

Bravo

AF:

0.0979

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.6

(source)

DANN

Benign

0.56

PhyloP100

0.19

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