dbSNP rs16940186: ENSG00000285040:n.227+8308A>G (chr16-85976134-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 ENST00000645754.1(ENSG00000285040):n.227+8308A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,348 control chromosomes in the GnomAD database, including 2,362 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 0.17 ( 2362 hom., cov: 32)

Consequence

ENSG00000285040
ENST00000645754.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.102

Publications

23 publications found

Variant links:

Genes affected

ENSG00000285040 (HGNC:):

ENSG00000285040 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 (SAS) allele frequency at 95% confidence interval = 0.269 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
ENSG00000285040	ENST00000645754.1 link	n.227+8308A>G		intron_variant	Intron 2 of 2
ENSG00000294410	ENST00000723428.1 link	n.410-1401T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25803

AN:

151242

Hom.:

2356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.171

AC:

25823

AN:

151348

Hom.:

2362

Cov.:

AF XY:

0.172

AC XY:

12751

AN XY:

73928

show subpopulations

African (AFR)

AF:

0.144

AC:

5954

AN:

41244

American (AMR)

AF:

0.178

AC:

2710

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1093

AN:

3468

East Asian (EAS)

AF:

0.251

AC:

1293

AN:

5160

South Asian (SAS)

AF:

0.281

AC:

1349

AN:

4800

European-Finnish (FIN)

AF:

0.147

AC:

1510

AN:

10282

Middle Eastern (MID)

AF:

0.310

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.164

AC:

11099

AN:

67872

Other (OTH)

AF:

0.200

AC:

421

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1077

2154

3232

4309

5386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.171

Hom.:

8671

Bravo

AF:

0.171

Asia WGS

AF:

0.257

AC:

888

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.61

(source)

DANN

Benign

0.36

PhyloP100

-0.10

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