Genetic Variant ENSG00000279622:n.241+252A>G (chr16-84924405-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 ENST00000625056.3(ENSG00000279622):n.241+252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,054 control chromosomes in the GnomAD database, including 7,939 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 ( 7939 hom., cov: 34)

Consequence

ENSG00000279622
ENST00000625056.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.965

Publications

2 publications found

Variant links:

Genes affected

ENSG00000279622 (HGNC:):

ENSG00000279622 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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
ENSG00000279622	ENST00000625056.3 link	n.241+252A>G	intron_variant	Intron 1 of 2	6
ENSG00000279622	ENST00000741212.1 link	n.131+374A>G	intron_variant	Intron 1 of 2
ENSG00000279622	ENST00000741213.1 link	n.115+374A>G	intron_variant	Intron 1 of 2
ENSG00000279622	ENST00000741214.1 link	n.157+374A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46533

AN:

151936

Hom.:

7918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.299

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

GnomAD4 genome

AF:

0.306

AC:

46602

AN:

152054

Hom.:

7939

Cov.:

AF XY:

0.305

AC XY:

22709

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.470

AC:

19493

AN:

41438

American (AMR)

AF:

0.311

AC:

4757

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

893

AN:

3468

East Asian (EAS)

AF:

0.188

AC:

970

AN:

5154

South Asian (SAS)

AF:

0.192

AC:

925

AN:

4828

European-Finnish (FIN)

AF:

0.234

AC:

2485

AN:

10598

Middle Eastern (MID)

AF:

0.253

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.238

AC:

16150

AN:

67968

Other (OTH)

AF:

0.297

AC:

627

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1612

3225

4837

6450

8062

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.138

Hom.:

264

Bravo

AF:

0.318

Asia WGS

AF:

0.220

AC:

765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.68

PhyloP100

-0.96

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