dbSNP rs10503852: ENSG00000305465:n.135-83A>G (chr8-29613159-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 ENST00000811158.1(ENSG00000305465):n.135-83A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,160 control chromosomes in the GnomAD database, including 4,187 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 0.23 ( 4187 hom., cov: 33)

Consequence

ENSG00000305465
ENST00000811158.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.100

Publications

2 publications found

Variant links:

Genes affected

ENSG00000305465 (HGNC:):

ENSG00000305465 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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
ENSG00000305465	ENST00000811158.1 link	n.135-83A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34782

AN:

152042

Hom.:

4180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.0269

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.241

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

GnomAD4 genome

AF:

0.229

AC:

34815

AN:

152160

Hom.:

4187

Cov.:

AF XY:

0.223

AC XY:

16599

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.245

AC:

10177

AN:

41508

American (AMR)

AF:

0.211

AC:

3232

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1036

AN:

3470

East Asian (EAS)

AF:

0.0268

AC:

139

AN:

5184

South Asian (SAS)

AF:

0.117

AC:

563

AN:

4812

European-Finnish (FIN)

AF:

0.228

AC:

2416

AN:

10586

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16422

AN:

67996

Other (OTH)

AF:

0.238

AC:

503

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1381

2762

4144

5525

6906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.236

Hom.:

2478

Bravo

AF:

0.233

Asia WGS

AF:

0.0820

AC:

287

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.54

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