Genetic Variant ENSG00000234261:n.373+61656G>T (chr6-14535858-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000729738.1(ENSG00000234261):n.373+61656G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,970 control chromosomes in the GnomAD database, including 19,555 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 0.48 ( 19555 hom., cov: 32)

Consequence

ENSG00000234261
ENST00000729738.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

1 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000234261	ENST00000729738.1 link	n.373+61656G>T	intron_variant	Intron 4 of 7
ENSG00000234261	ENST00000729739.1 link	n.309+61656G>T	intron_variant	Intron 4 of 7
ENSG00000234261	ENST00000729740.1 link	n.270+61656G>T	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72623

AN:

151852

Hom.:

19502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.717

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.654

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.410

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

GnomAD4 genome

AF:

0.479

AC:

72747

AN:

151970

Hom.:

19555

Cov.:

AF XY:

0.480

AC XY:

35652

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.717

AC:

29725

AN:

41440

American (AMR)

AF:

0.452

AC:

6905

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

1034

AN:

3466

East Asian (EAS)

AF:

0.653

AC:

3357

AN:

5142

South Asian (SAS)

AF:

0.558

AC:

2692

AN:

4824

European-Finnish (FIN)

AF:

0.354

AC:

3741

AN:

10568

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.352

AC:

23911

AN:

67948

Other (OTH)

AF:

0.414

AC:

873

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1734

3467

5201

6934

8668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.400

Hom.:

37184

Bravo

AF:

0.497

Asia WGS

AF:

0.614

AC:

2130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.57

(source)

DANN

Benign

0.23

PhyloP100

0.26

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