dbSNP rs978724: ENSG00000228714:n.322-19138C>A (chr9-115760700-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000832032.1(ENSG00000228714):n.322-19138C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 152,026 control chromosomes in the GnomAD database, including 48 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 0.015 ( 48 hom., cov: 32)

Consequence

ENSG00000228714
ENST00000832032.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335

Publications

0 publications found

Variant links:

Genes affected

ENSG00000228714 (HGNC:):

ENSG00000228714 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376234	XR_930269.2 link	n.366+12974G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228714	ENST00000832032.1 link	n.322-19138C>A	intron_variant	Intron 1 of 2
ENSG00000308189	ENST00000832372.1 link	n.305+12974G>T	intron_variant	Intron 2 of 3
ENSG00000308189	ENST00000832373.1 link	n.334+12974G>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0154

AC:

2342

AN:

151908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00317

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0170

Gnomad ASJ

AF:

0.0208

Gnomad EAS

AF:

0.0894

Gnomad SAS

AF:

0.0609

Gnomad FIN

AF:

0.00490

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0148

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

GnomAD4 genome

AF:

0.0154

AC:

2341

AN:

152026

Hom.:

Cov.:

AF XY:

0.0166

AC XY:

1230

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.00316

AC:

131

AN:

41508

American (AMR)

AF:

0.0169

AC:

258

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.0208

AC:

AN:

3468

East Asian (EAS)

AF:

0.0892

AC:

459

AN:

5144

South Asian (SAS)

AF:

0.0609

AC:

294

AN:

4826

European-Finnish (FIN)

AF:

0.00490

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0152

AC:

1034

AN:

67926

Other (OTH)

AF:

0.0147

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

113

227

340

454

567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0151

Hom.:

Bravo

AF:

0.0153

Asia WGS

AF:

0.0660

AC:

229

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.60

(source)

DANN

Benign

0.31

PhyloP100

-0.34

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