Genetic Variant GS1-204I12.4:n.858+1465T>C (chr1-185675531-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000785885.1(GS1-204I12.4):n.858+1465T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 152,254 control chromosomes in the GnomAD database, including 414 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 0.047 ( 414 hom., cov: 32)

Consequence

GS1-204I12.4
ENST00000785885.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.94

Publications

3 publications found

Variant links:

Genes affected

GS1-204I12.4 (HGNC:):

GS1-204I12.4 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985239	XR_001738340.2 link	n.1067-3918T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
GS1-204I12.4	ENST00000785885.1 link	n.858+1465T>C	intron_variant	Intron 4 of 6
GS1-204I12.4	ENST00000785886.1 link	n.169-3918T>C	intron_variant	Intron 2 of 3
GS1-204I12.4	ENST00000785887.1 link	n.124-3918T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0472

AC:

7182

AN:

152136

Hom.:

404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0501

Gnomad EAS

AF:

0.0464

Gnomad SAS

AF:

0.0325

Gnomad FIN

AF:

0.0102

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00753

Gnomad OTH

AF:

0.0511

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

GnomAD4 genome

AF:

0.0474

AC:

7218

AN:

152254

Hom.:

414

Cov.:

AF XY:

0.0459

AC XY:

3420

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.133

AC:

5533

AN:

41532

American (AMR)

AF:

0.0243

AC:

372

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0501

AC:

174

AN:

3472

East Asian (EAS)

AF:

0.0467

AC:

242

AN:

5182

South Asian (SAS)

AF:

0.0325

AC:

157

AN:

4830

European-Finnish (FIN)

AF:

0.0102

AC:

108

AN:

10626

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00753

AC:

512

AN:

68008

Other (OTH)

AF:

0.0506

AC:

107

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

347

694

1042

1389

1736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0208

Hom.:

489

Bravo

AF:

0.0543

Asia WGS

AF:

0.0660

AC:

231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.014

(source)

DANN

Benign

0.60

PhyloP100

-1.9

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