dbSNP rs1339896: ENSG00000287856:c.30+18132G>C (chr1-231444306-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000662216.1(ENSG00000287856):c.30+18132G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,080 control chromosomes in the GnomAD database, including 5,466 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 0.26 ( 5466 hom., cov: 32)

Consequence

ENSG00000287856
ENST00000662216.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Publications

2 publications found

Variant links:

Genes affected

ENSG00000287856 (HGNC:):

ENSG00000287856 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=-0.76).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
ENSG00000287856	ENST00000662216.1 link	c.30+18132G>C	intron_variant	Intron 3 of 6	ENSP00000499467.1
ENSG00000287856	ENST00000653908.1 link	c.30+18132G>C	intron_variant	Intron 2 of 4	ENSP00000499669.1
ENSG00000287856	ENST00000653198.1 link	n.433+18166G>C	intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39455

AN:

151962

Hom.:

5456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.0362

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.260

AC:

39494

AN:

152080

Hom.:

5466

Cov.:

AF XY:

0.251

AC XY:

18652

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.297

AC:

12333

AN:

41494

American (AMR)

AF:

0.314

AC:

4791

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

799

AN:

3470

East Asian (EAS)

AF:

0.0361

AC:

187

AN:

5182

South Asian (SAS)

AF:

0.119

AC:

574

AN:

4822

European-Finnish (FIN)

AF:

0.183

AC:

1934

AN:

10556

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

18037

AN:

67968

Other (OTH)

AF:

0.244

AC:

514

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1458

2916

4373

5831

7289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.258

Hom.:

636

Bravo

AF:

0.276

Asia WGS

AF:

0.0960

AC:

338

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.5

(source)

DANN

Benign

0.66

PhyloP100

0.30

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