Genetic Variant ENSG00000300787:n.406+55390G>T (chr9-23908716-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000774067.1(ENSG00000300787):n.406+55390G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,154 control chromosomes in the GnomAD database, including 329 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 0.042 ( 329 hom., cov: 32)

Consequence

ENSG00000300787
ENST00000774067.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.171

Variant links:

Genes affected

ENSG00000300787 (HGNC:):

ENSG00000300787 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375993	XR_929520.3 link	n.460-37277G>T		intron_variant	Intron 2 of 4
LOC105375993	XR_929521.3 link	n.460-37277G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300787	ENST00000774067.1 link	n.406+55390G>T	intron_variant	Intron 2 of 2
ENSG00000300787	ENST00000850877.1 link	n.407-37277G>T	intron_variant	Intron 2 of 6
ENSG00000300787	ENST00000850878.1 link	n.406+55390G>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6415

AN:

152036

Hom.:

317

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0781

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.0151

Gnomad FIN

AF:

0.0228

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00302

Gnomad OTH

AF:

0.0360

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

GnomAD4 genome

AF:

0.0424

AC:

6456

AN:

152154

Hom.:

329

Cov.:

AF XY:

0.0447

AC XY:

3324

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0783

AC:

3250

AN:

41516

American (AMR)

AF:

0.126

AC:

1924

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3470

East Asian (EAS)

AF:

0.128

AC:

660

AN:

5170

South Asian (SAS)

AF:

0.0151

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0228

AC:

242

AN:

10600

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00302

AC:

205

AN:

67982

Other (OTH)

AF:

0.0447

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

281

562

843

1124

1405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00839

Hom.:

Bravo

AF:

0.0552

Asia WGS

AF:

0.0850

AC:

295

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.9

(source)

DANN

Benign

0.40

PhyloP100

0.17

Splicing

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

Publications

Loading publications...

9-23908716-G-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over