Genetic Variant ENSG00000231873:n.302-2627C>T (chr3-40859765-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 ENST00000412811.2(ENSG00000231873):n.302-2627C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 152,238 control chromosomes in the GnomAD database, including 876 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 0.083 ( 876 hom., cov: 33)

Consequence

ENSG00000231873
ENST00000412811.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.941

Publications

0 publications found

Variant links:

Genes affected

ENSG00000231873 (HGNC:):

ENSG00000231873 links:

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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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377043	XR_007095885.1 link	n.266-51183C>T		intron_variant	Intron 2 of 2
LOC105377043	XR_940766.3 link	n.266-10119C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231873	ENST00000412811.2 link	n.302-2627C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.0833

AC:

12671

AN:

152120

Hom.:

869

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0738

Gnomad ASJ

AF:

0.0378

Gnomad EAS

AF:

0.0292

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.0160

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0428

Gnomad OTH

AF:

0.0737

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

GnomAD4 genome

AF:

0.0835

AC:

12707

AN:

152238

Hom.:

876

Cov.:

AF XY:

0.0809

AC XY:

6021

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.192

AC:

7976

AN:

41510

American (AMR)

AF:

0.0738

AC:

1129

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0378

AC:

131

AN:

3470

East Asian (EAS)

AF:

0.0291

AC:

151

AN:

5194

South Asian (SAS)

AF:

0.0129

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0160

AC:

170

AN:

10610

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0428

AC:

2909

AN:

68018

Other (OTH)

AF:

0.0729

AC:

154

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

552

1103

1655

2206

2758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0514

Hom.:

753

Bravo

AF:

0.0923

Asia WGS

AF:

0.0420

AC:

148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

5.5

(source)

DANN

Benign

0.29

PhyloP100

0.94

Mutation Taster

=100/0

polymorphism

(source)

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