Genetic Variant ENSG00000230309:n.1038-31224C>T (chr6-78235177-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715178.1(ENSG00000230309):n.1038-31224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,152 control chromosomes in the GnomAD database, including 1,024 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 ( 1024 hom., cov: 32)

Consequence

ENSG00000230309
ENST00000715178.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100

Publications

4 publications found

Variant links:

Genes affected

ENSG00000230309 (HGNC:):

ENSG00000230309 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2 link	n.135-31224C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1 link	n.1038-31224C>T		intron_variant	Intron 6 of 14

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17255

AN:

152034

Hom.:

1024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0876

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.117

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

GnomAD4 genome

AF:

0.113

AC:

17243

AN:

152152

Hom.:

1024

Cov.:

AF XY:

0.111

AC XY:

8231

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.112

AC:

4653

AN:

41536

American (AMR)

AF:

0.0875

AC:

1337

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

696

AN:

3470

East Asian (EAS)

AF:

0.149

AC:

771

AN:

5158

South Asian (SAS)

AF:

0.105

AC:

507

AN:

4822

European-Finnish (FIN)

AF:

0.0626

AC:

663

AN:

10584

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8216

AN:

67980

Other (OTH)

AF:

0.115

AC:

244

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

780

1560

2340

3120

3900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<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:

0.116

Hom.:

215

Bravo

AF:

0.115

Asia WGS

AF:

0.146

AC:

506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.8

(source)

DANN

Benign

0.38

PhyloP100

0.10

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