Genetic Variant ENST00000785885.1:n.858+800C>T (chr1-185674866-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000785885.1(GS1-204I12.4):n.858+800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,174 control chromosomes in the GnomAD database, including 390 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 0.045 ( 390 hom., cov: 32)

Consequence

GS1-204I12.4
ENST00000785885.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360

Publications

1 publications found

Variant links:

Genes affected

GS1-204I12.4 (HGNC:):

GS1-204I12.4 links:

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new If you want to explore the variant's impact on the transcript ENST00000785885.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785885.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	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
GS1-204I12.4	ENST00000785885.1	n.858+800C>T	intron	N/A
GS1-204I12.4	ENST00000785886.1	n.169-4583C>T	intron	N/A
GS1-204I12.4	ENST00000785887.1	n.124-4583C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0452

AC:

6877

AN:

152056

Hom.:

382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0240

Gnomad ASJ

AF:

0.0502

Gnomad EAS

AF:

0.0352

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.00208

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00715

Gnomad OTH

AF:

0.0492

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

GnomAD4 genome

AF:

0.0454

AC:

6908

AN:

152174

Hom.:

390

Cov.:

AF XY:

0.0439

AC XY:

3263

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.130

AC:

5407

AN:

41486

American (AMR)

AF:

0.0239

AC:

365

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0502

AC:

174

AN:

3468

East Asian (EAS)

AF:

0.0351

AC:

182

AN:

5180

South Asian (SAS)

AF:

0.0323

AC:

156

AN:

4830

European-Finnish (FIN)

AF:

0.00208

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00715

AC:

486

AN:

68006

Other (OTH)

AF:

0.0487

AC:

103

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

305

610

915

1220

1525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0345

Hom.:

Bravo

AF:

0.0526

Asia WGS

AF:

0.0540

AC:

188

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.44

(source)

DANN

Benign

0.50

PhyloP100

-0.036

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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