Genetic Variant ENST00000661266.1:n.1311-1036A>G (chr8-134192893-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 ENST00000661266.1(ENSG00000288067):n.1311-1036A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,194 control chromosomes in the GnomAD database, including 2,534 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 0.18 ( 2534 hom., cov: 32)

Consequence

ENSG00000288067
ENST00000661266.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.315

Publications

1 publications found

Variant links:

Genes affected

ENSG00000288067 (HGNC:):

ENSG00000288067 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000288067	ENST00000661266.1 link	n.1311-1036A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26787

AN:

152076

Hom.:

2533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.180

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

GnomAD4 genome

AF:

0.176

AC:

26795

AN:

152194

Hom.:

2534

Cov.:

AF XY:

0.178

AC XY:

13253

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.217

AC:

9010

AN:

41514

American (AMR)

AF:

0.225

AC:

3436

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

376

AN:

3470

East Asian (EAS)

AF:

0.306

AC:

1581

AN:

5174

South Asian (SAS)

AF:

0.175

AC:

844

AN:

4832

European-Finnish (FIN)

AF:

0.117

AC:

1238

AN:

10594

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.143

AC:

9739

AN:

68002

Other (OTH)

AF:

0.178

AC:

376

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1139

2278

3416

4555

5694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.154

Hom.:

3170

Bravo

AF:

0.189

Asia WGS

AF:

0.208

AC:

720

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.9

(source)

DANN

Benign

0.84

PhyloP100

-0.32

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