Genetic Variant ENSG00000299137:n.316-14217C>G (chr2-234260381-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000760713.1(ENSG00000299137):n.316-14217C>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 152,244 control chromosomes in the GnomAD database, including 2,929 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 ( 2929 hom., cov: 32)

Consequence

ENSG00000299137
ENST00000760713.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.128

Publications

1 publications found

Variant links:

COSMIC-nc: COSV69023816

Genes affected

ENSG00000299137 (HGNC:):

ENSG00000299137 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 (AMR) allele frequency at 95% confidence interval = 0.251 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
ENSG00000299137	ENST00000760713.1 link	n.316-14217C>G		intron_variant	Intron 2 of 2
ENSG00000299137	ENST00000760714.1 link	n.341-962C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26731

AN:

152126

Hom.:

2930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0628

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.176

AC:

26723

AN:

152244

Hom.:

2929

Cov.:

AF XY:

0.176

AC XY:

13120

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0627

AC:

2605

AN:

41572

American (AMR)

AF:

0.257

AC:

3934

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

698

AN:

3468

East Asian (EAS)

AF:

0.00270

AC:

AN:

5182

South Asian (SAS)

AF:

0.171

AC:

825

AN:

4820

European-Finnish (FIN)

AF:

0.180

AC:

1907

AN:

10602

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.236

AC:

16078

AN:

68000

Other (OTH)

AF:

0.172

AC:

363

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1107

2213

3320

4426

5533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.199

Hom.:

444

Bravo

AF:

0.175

Asia WGS

AF:

0.0810

AC:

280

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

5.4

(source)

DANN

Benign

0.49

PhyloP100

0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-234260381-G-C

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