Genetic Variant ENSG00000230960:n.357+8406C>T (chr6-170177401-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 ENST00000691159.1(ENSG00000230960):n.357+8406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.089 ( 536 hom., cov: 20)

Consequence

ENSG00000230960
ENST00000691159.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.983

Publications

2 publications found

Variant links:

Genes affected

ENSG00000230960 (HGNC:):

ENSG00000230960 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691159.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000230960	ENST00000691159.1	n.357+8406C>T	intron	N/A
ENSG00000230960	ENST00000701993.1	n.382+8337C>T	intron	N/A
ENSG00000230960	ENST00000843770.1	n.475+8406C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0886

AC:

7673

AN:

86598

Hom.:

534

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.0103

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0449

Gnomad EAS

AF:

0.00216

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.0469

Gnomad MID

AF:

0.183

Gnomad NFE

AF:

0.0889

Gnomad OTH

AF:

0.0936

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

GnomAD4 genome

AF:

0.0886

AC:

7678

AN:

86658

Hom.:

536

Cov.:

AF XY:

0.0875

AC XY:

3659

AN XY:

41834

show subpopulations

African (AFR)

AF:

0.108

AC:

2505

AN:

23090

American (AMR)

AF:

0.103

AC:

815

AN:

7914

Ashkenazi Jewish (ASJ)

AF:

0.0449

AC:

AN:

2118

East Asian (EAS)

AF:

0.00217

AC:

AN:

3230

South Asian (SAS)

AF:

0.104

AC:

269

AN:

2582

European-Finnish (FIN)

AF:

0.0469

AC:

266

AN:

5668

Middle Eastern (MID)

AF:

0.203

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.0889

AC:

3583

AN:

40308

Other (OTH)

AF:

0.0944

AC:

107

AN:

1134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

307

614

920

1227

1534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.5

(source)

DANN

Benign

0.62

PhyloP100

-0.98

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over