dbSNP rs3744728: ENSG00000262231: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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