Genetic Variant ENSG00000292977:n.81+10620C>T (chr3-36801658-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 ENST00000753312.1(ENSG00000292977):n.81+10620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,126 control chromosomes in the GnomAD database, including 7,617 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 0.31 ( 7617 hom., cov: 33)

Consequence

ENSG00000292977
ENST00000753312.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

9 publications found

Variant links:

Genes affected

ENSG00000292977 (HGNC:):

ENSG00000292977 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=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000292977	ENST00000753312.1 link	n.81+10620C>T	intron_variant	Intron 1 of 4
ENSG00000292977	ENST00000753313.1 link	n.79+10620C>T	intron_variant	Intron 1 of 5
ENSG00000292977	ENST00000753314.1 link	n.76+10620C>T	intron_variant	Intron 1 of 4
ENSG00000292977	ENST00000753315.1 link	n.80+10620C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46901

AN:

152008

Hom.:

7609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.0609

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.306

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

GnomAD4 genome

AF:

0.309

AC:

46939

AN:

152126

Hom.:

7617

Cov.:

AF XY:

0.304

AC XY:

22640

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.272

AC:

11282

AN:

41482

American (AMR)

AF:

0.335

AC:

5119

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

983

AN:

3468

East Asian (EAS)

AF:

0.0608

AC:

316

AN:

5194

South Asian (SAS)

AF:

0.283

AC:

1364

AN:

4820

European-Finnish (FIN)

AF:

0.299

AC:

3165

AN:

10570

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23667

AN:

67980

Other (OTH)

AF:

0.304

AC:

644

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1656

3312

4967

6623

8279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.332

Hom.:

17183

Bravo

AF:

0.306

Asia WGS

AF:

0.193

AC:

673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

1.6

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