dbSNP rs3860306: ENSG00000302138:n.654-17459T>C (chr1-189468052-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 ENST00000784625.1(ENSG00000302138):n.654-17459T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,130 control chromosomes in the GnomAD database, including 2,380 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 0.15 ( 2380 hom., cov: 32)

Consequence

ENSG00000302138
ENST00000784625.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

Publications

3 publications found

Variant links:

Genes affected

ENSG00000302138 (HGNC:):

ENSG00000302138 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 (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371657	XR_002958413.2 link	n.483-100277T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302138	ENST00000784625.1 link	n.654-17459T>C	intron_variant	Intron 5 of 5
ENSG00000302138	ENST00000784626.1 link	n.642-17459T>C	intron_variant	Intron 4 of 4
ENSG00000302138	ENST00000784627.1 link	n.612-17459T>C	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23497

AN:

152014

Hom.:

2379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0384

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0514

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.154

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

GnomAD4 genome

AF:

0.154

AC:

23494

AN:

152130

Hom.:

2380

Cov.:

AF XY:

0.153

AC XY:

11376

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0383

AC:

1589

AN:

41542

American (AMR)

AF:

0.141

AC:

2147

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

752

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5164

South Asian (SAS)

AF:

0.0514

AC:

248

AN:

4824

European-Finnish (FIN)

AF:

0.276

AC:

2914

AN:

10556

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.222

AC:

15100

AN:

67992

Other (OTH)

AF:

0.153

AC:

323

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

965

1930

2894

3859

4824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.187

Hom.:

4515

Bravo

AF:

0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.2

(source)

DANN

Benign

0.76

PhyloP100

0.032

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