dbSNP rs12483177: ENSG00000310337:n.309+1468G>C (chr21-43342571-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 ENST00000849138.1(ENSG00000310337):n.309+1468G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,024 control chromosomes in the GnomAD database, including 3,802 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 0.22 ( 3802 hom., cov: 33)

Consequence

ENSG00000310337
ENST00000849138.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.687

Publications

1 publications found

Variant links:

Genes affected

ENSG00000310337 (HGNC:):

ENSG00000310337 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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
ENSG00000310337	ENST00000849138.1 link	n.309+1468G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33518

AN:

151906

Hom.:

3798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.214

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

GnomAD4 genome

AF:

0.221

AC:

33551

AN:

152024

Hom.:

3802

Cov.:

AF XY:

0.216

AC XY:

16032

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.242

AC:

10038

AN:

41432

American (AMR)

AF:

0.185

AC:

2832

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1029

AN:

3470

East Asian (EAS)

AF:

0.175

AC:

903

AN:

5160

South Asian (SAS)

AF:

0.213

AC:

1026

AN:

4816

European-Finnish (FIN)

AF:

0.159

AC:

1678

AN:

10582

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.224

AC:

15244

AN:

67980

Other (OTH)

AF:

0.215

AC:

451

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1308

2616

3925

5233

6541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.113

Hom.:

192

Bravo

AF:

0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.63

(source)

DANN

Benign

0.23

PhyloP100

-0.69

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