Genetic Variant ENST00000728931.1:n.557-2466G>A (chr10-42766813-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000728931.1(ENSG00000295267):n.557-2466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,078 control chromosomes in the GnomAD database, including 1,091 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 0.11 ( 1091 hom., cov: 32)

Consequence

ENSG00000295267
ENST00000728931.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

6 publications found

Variant links:

Genes affected

ENSG00000295267 (HGNC:):

ENSG00000295267 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378269	NR_134498.1 link	n.285-2466G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295267	ENST00000728931.1 link	n.557-2466G>A		intron_variant	Intron 1 of 1
ENSG00000295267	ENST00000728932.1 link	n.237-2466G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16735

AN:

151960

Hom.:

1080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.0253

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0743

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.110

AC:

16770

AN:

152078

Hom.:

1091

Cov.:

AF XY:

0.112

AC XY:

8333

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.176

AC:

7318

AN:

41462

American (AMR)

AF:

0.111

AC:

1697

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

444

AN:

3468

East Asian (EAS)

AF:

0.0247

AC:

128

AN:

5174

South Asian (SAS)

AF:

0.136

AC:

653

AN:

4818

European-Finnish (FIN)

AF:

0.113

AC:

1190

AN:

10570

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0743

AC:

5051

AN:

68002

Other (OTH)

AF:

0.103

AC:

217

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

734

1468

2201

2935

3669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.0896

Hom.:

400

Bravo

AF:

0.113

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.99

(source)

DANN

Benign

0.67

PhyloP100

-1.3

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