Genetic Variant ENSG00000302346:n.270+2178G>A (chr5-67979460-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 ENST00000785994.1(ENSG00000302346):n.270+2178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,112 control chromosomes in the GnomAD database, including 2,725 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 0.17 ( 2725 hom., cov: 33)

Consequence

ENSG00000302346
ENST00000785994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Publications

3 publications found

Variant links:

Genes affected

ENSG00000302346 (HGNC:):

ENSG00000302346 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986420	XR_001742692.1 link	n.146+2178G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302346	ENST00000785994.1 link	n.270+2178G>A		intron_variant	Intron 3 of 5
ENSG00000302346	ENST00000785995.1 link	n.303+2178G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25941

AN:

151996

Hom.:

2725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0812

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0277

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.161

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

GnomAD4 genome

AF:

0.171

AC:

25950

AN:

152112

Hom.:

2725

Cov.:

AF XY:

0.171

AC XY:

12718

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0813

AC:

3374

AN:

41522

American (AMR)

AF:

0.127

AC:

1939

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

577

AN:

3472

East Asian (EAS)

AF:

0.0274

AC:

142

AN:

5186

South Asian (SAS)

AF:

0.105

AC:

507

AN:

4814

European-Finnish (FIN)

AF:

0.292

AC:

3089

AN:

10576

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15679

AN:

67952

Other (OTH)

AF:

0.160

AC:

338

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1080

2160

3240

4320

5400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.198

Hom.:

2173

Bravo

AF:

0.153

Asia WGS

AF:

0.0790

AC:

275

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.0

(source)

DANN

Benign

0.79

PhyloP100

0.32

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