Genetic Variant ENSG00000253406:n.116+8700A>G (chr5-149267990-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 ENST00000523176.1(ENSG00000253406):n.116+8700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,180 control chromosomes in the GnomAD database, including 762 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 0.094 ( 762 hom., cov: 32)

Consequence

ENSG00000253406
ENST00000523176.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Publications

6 publications found

Variant links:

Genes affected

ENSG00000253406 (HGNC:):

ENSG00000253406 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000253406	ENST00000523176.1 link	n.116+8700A>G	intron_variant	Intron 1 of 1	1
ENSG00000248647	ENST00000512647.2 link	n.73+8700A>G	intron_variant	Intron 1 of 2	3
ENSG00000248647	ENST00000522685.1 link	n.87+8700A>G	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0937

AC:

14243

AN:

152062

Hom.:

761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0798

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.0856

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0954

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.0820

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.0935

AC:

14233

AN:

152180

Hom.:

762

Cov.:

AF XY:

0.0964

AC XY:

7174

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0797

AC:

3306

AN:

41504

American (AMR)

AF:

0.0854

AC:

1305

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

688

AN:

3464

East Asian (EAS)

AF:

0.207

AC:

1070

AN:

5176

South Asian (SAS)

AF:

0.0946

AC:

456

AN:

4820

European-Finnish (FIN)

AF:

0.126

AC:

1338

AN:

10598

Middle Eastern (MID)

AF:

0.219

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0820

AC:

5576

AN:

68020

Other (OTH)

AF:

0.115

AC:

243

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

646

1292

1937

2583

3229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.0866

Hom.:

751

Bravo

AF:

0.0910

Asia WGS

AF:

0.146

AC:

505

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.7

(source)

DANN

Benign

0.54

PhyloP100

0.10

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