dbSNP rs9772321: ENSG00000283674:n.937+25000A>G (chr8-12634130-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 ENST00000637678.1(ENSG00000283674):n.937+25000A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 149,712 control chromosomes in the GnomAD database, including 4,883 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 0.24 ( 4883 hom., cov: 31)

Consequence

ENSG00000283674
ENST00000637678.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.160

Publications

0 publications found

Variant links:

Genes affected

ENSG00000283674 (HGNC:):

ENSG00000283674 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC729732	NR_047662.2 link	n.1034+25000A>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000283674	ENST00000637678.1 link	n.937+25000A>G	intron_variant	Intron 2 of 5	1
ENSG00000283674	ENST00000635775.1 link	n.1011+25000A>G	intron_variant	Intron 2 of 8	2
ENSG00000283674	ENST00000636990.2 link	n.523-7560A>G	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35220

AN:

149596

Hom.:

4876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.0541

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.235

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

GnomAD4 genome

AF:

0.235

AC:

35238

AN:

149712

Hom.:

4883

Cov.:

AF XY:

0.231

AC XY:

16881

AN XY:

73192

show subpopulations

African (AFR)

AF:

0.202

AC:

8007

AN:

39580

American (AMR)

AF:

0.271

AC:

4100

AN:

15116

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

964

AN:

3446

East Asian (EAS)

AF:

0.0538

AC:

277

AN:

5148

South Asian (SAS)

AF:

0.162

AC:

775

AN:

4796

European-Finnish (FIN)

AF:

0.209

AC:

2200

AN:

10528

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.268

AC:

18174

AN:

67812

Other (OTH)

AF:

0.236

AC:

493

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1319

2639

3958

5278

6597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.263

Hom.:

918

Asia WGS

AF:

0.124

AC:

432

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.51

PhyloP100

-0.16

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