dbSNP rs1765811: ENSG00000287856:c.30+6214C>T (chr1-231456224-G-A) – 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+6214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,110 control chromosomes in the GnomAD database, including 9,056 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 0.32 ( 9056 hom., cov: 32)

Consequence

ENSG00000287856
ENST00000662216.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

3 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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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	UniProt
ENSG00000287856	ENST00000662216.1 link	c.30+6214C>T	intron_variant	Intron 3 of 6	ENSP00000499467.1	A0A590UJK7
ENSG00000287856	ENST00000653908.1 link	c.30+6214C>T	intron_variant	Intron 2 of 4	ENSP00000499669.1	A0A590UK27
ENSG00000287856	ENST00000653198.1 link	n.433+6248C>T	intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48406

AN:

151992

Hom.:

9029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.502

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.0362

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.290

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

GnomAD4 genome

AF:

0.319

AC:

48481

AN:

152110

Hom.:

9056

Cov.:

AF XY:

0.308

AC XY:

22900

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.502

AC:

20823

AN:

41460

American (AMR)

AF:

0.336

AC:

5136

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

799

AN:

3472

East Asian (EAS)

AF:

0.0361

AC:

187

AN:

5186

South Asian (SAS)

AF:

0.121

AC:

582

AN:

4828

European-Finnish (FIN)

AF:

0.183

AC:

1938

AN:

10580

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18080

AN:

67988

Other (OTH)

AF:

0.287

AC:

605

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1618

3236

4854

6472

8090

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.309

Hom.:

1258

Bravo

AF:

0.344

Asia WGS

AF:

0.113

AC:

398

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.9

(source)

DANN

Benign

0.85

PhyloP100

0.12

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