dbSNP rs724767: ENSG00000238043:n.330-1321C>T (chr3-194004541-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000426616.1(ENSG00000238043):n.330-1321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,150 control chromosomes in the GnomAD database, including 1,466 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 0.13 ( 1466 hom., cov: 32)

Consequence

ENSG00000238043
ENST00000426616.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810

Publications

15 publications found

Variant links:

Genes affected

ENSG00000238043 (HGNC:):

ENSG00000238043 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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
ENSG00000238043	ENST00000426616.1 link	n.330-1321C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20194

AN:

152030

Hom.:

1457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.133

AC:

20233

AN:

152150

Hom.:

1466

Cov.:

AF XY:

0.133

AC XY:

9917

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.183

AC:

7573

AN:

41480

American (AMR)

AF:

0.147

AC:

2243

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

422

AN:

3472

East Asian (EAS)

AF:

0.156

AC:

805

AN:

5172

South Asian (SAS)

AF:

0.138

AC:

666

AN:

4826

European-Finnish (FIN)

AF:

0.122

AC:

1295

AN:

10588

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6850

AN:

68018

Other (OTH)

AF:

0.119

AC:

252

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

886

1773

2659

3546

4432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.118

Hom.:

2280

Bravo

AF:

0.139

Asia WGS

AF:

0.162

AC:

562

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.5

(source)

DANN

Benign

0.61

PhyloP100

-0.081

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