Genetic Variant ENSG00000234261:n.205-12358G>A (chr6-14802456-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000629853.3(ENSG00000234261):n.205-12358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,130 control chromosomes in the GnomAD database, including 2,031 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 0.11 ( 2031 hom., cov: 32)

Consequence

ENSG00000234261
ENST00000629853.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

Publications

3 publications found

Variant links:

Genes affected

ENSG00000234261 (HGNC:):

ENSG00000234261 links:

Genome browser will be placed here

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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
ENSG00000234261	ENST00000629853.3 link	n.205-12358G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16766

AN:

152012

Hom.:

2016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0929

Gnomad ASJ

AF:

0.0315

Gnomad EAS

AF:

0.0179

Gnomad SAS

AF:

0.0961

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0287

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.0822

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

GnomAD4 genome

AF:

0.111

AC:

16829

AN:

152130

Hom.:

2031

Cov.:

AF XY:

0.108

AC XY:

8031

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.298

AC:

12357

AN:

41452

American (AMR)

AF:

0.0933

AC:

1427

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0315

AC:

109

AN:

3464

East Asian (EAS)

AF:

0.0178

AC:

AN:

5176

South Asian (SAS)

AF:

0.0960

AC:

463

AN:

4824

European-Finnish (FIN)

AF:

0.0185

AC:

196

AN:

10596

Middle Eastern (MID)

AF:

0.0308

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0287

AC:

1950

AN:

68010

Other (OTH)

AF:

0.0809

AC:

171

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

651

1301

1952

2602

3253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0498

Hom.:

956

Bravo

AF:

0.124

Asia WGS

AF:

0.0770

AC:

268

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.19

(source)

DANN

Benign

0.55

PhyloP100

-2.5

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