dbSNP rs724841: ENSG00000295016:n.*87C>T (chr2-107003786-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 ENST00000727380.1(ENSG00000295016):n.*87C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,056 control chromosomes in the GnomAD database, including 5,964 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 ( 5964 hom., cov: 32)

Consequence

ENSG00000295016
ENST00000727380.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

Publications

2 publications found

Variant links:

Genes affected

ENSG00000295016 (HGNC:):

ENSG00000295016 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295016	ENST00000727380.1 link	n.*87C>T		downstream_gene_variant
ENSG00000295016	ENST00000727381.1 link	n.*81C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40278

AN:

151938

Hom.:

5967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.445

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.286

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

GnomAD4 genome

AF:

0.265

AC:

40279

AN:

152056

Hom.:

5964

Cov.:

AF XY:

0.264

AC XY:

19605

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.141

AC:

5847

AN:

41482

American (AMR)

AF:

0.257

AC:

3927

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.445

AC:

1545

AN:

3472

East Asian (EAS)

AF:

0.255

AC:

1314

AN:

5156

South Asian (SAS)

AF:

0.266

AC:

1281

AN:

4818

European-Finnish (FIN)

AF:

0.260

AC:

2739

AN:

10554

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22669

AN:

67976

Other (OTH)

AF:

0.284

AC:

598

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1453

2906

4360

5813

7266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.312

Hom.:

4888

Bravo

AF:

0.258

Asia WGS

AF:

0.232

AC:

807

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.54

(source)

DANN

Benign

0.48

PhyloP100

-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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