dbSNP rs1076039: ENSG00000306739:n.389+5187T>A (chr17-4622476-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000820607.1(ENSG00000306739):n.389+5187T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,116 control chromosomes in the GnomAD database, including 1,102 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 0.11 ( 1102 hom., cov: 32)

Consequence

ENSG00000306739
ENST00000820607.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670

Publications

1 publications found

Variant links:

Genes affected

ENSG00000306739 (HGNC:):

ENSG00000306739 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=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371498	XR_001752766.3 link	n.236+5187T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306739	ENST00000820607.1 link	n.389+5187T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16211

AN:

151998

Hom.:

1102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0292

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0466

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.107

AC:

16213

AN:

152116

Hom.:

1102

Cov.:

AF XY:

0.104

AC XY:

7770

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0291

AC:

1206

AN:

41492

American (AMR)

AF:

0.140

AC:

2133

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

437

AN:

3470

East Asian (EAS)

AF:

0.00174

AC:

AN:

5176

South Asian (SAS)

AF:

0.0465

AC:

224

AN:

4822

European-Finnish (FIN)

AF:

0.122

AC:

1289

AN:

10582

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.154

AC:

10442

AN:

67982

Other (OTH)

AF:

0.124

AC:

261

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

720

1440

2161

2881

3601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.125

Hom.:

162

Bravo

AF:

0.104

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.9

(source)

DANN

Benign

0.89

PhyloP100

0.067

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