Genetic Variant ENSG00000303408:n.137+4707C>T (chr1-143665797-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000794270.1(ENSG00000303408):n.137+4707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 147,412 control chromosomes in the GnomAD database, including 1,283 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 0.060 ( 1283 hom., cov: 30)

Consequence

ENSG00000303408
ENST00000794270.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.93

Publications

5 publications found

Variant links:

Genes affected

ENSG00000303408 (HGNC:):

ENSG00000303408 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904406	XR_007066578.1 link	n.121+4707C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303408	ENST00000794270.1 link	n.137+4707C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0598

AC:

8811

AN:

147296

Hom.:

1281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0209

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000202

Gnomad SAS

AF:

0.00134

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0130

Gnomad NFE

AF:

0.000591

Gnomad OTH

AF:

0.0485

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

GnomAD4 genome

AF:

0.0599

AC:

8830

AN:

147412

Hom.:

1283

Cov.:

AF XY:

0.0581

AC XY:

4173

AN XY:

71862

show subpopulations

African (AFR)

AF:

0.207

AC:

8378

AN:

40504

American (AMR)

AF:

0.0208

AC:

306

AN:

14702

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3414

East Asian (EAS)

AF:

0.000203

AC:

AN:

4932

South Asian (SAS)

AF:

0.00134

AC:

AN:

4470

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10182

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.000591

AC:

AN:

65998

Other (OTH)

AF:

0.0481

AC:

AN:

2018

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

311

622

932

1243

1554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<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:

0.00759

Hom.:

Asia WGS

AF:

0.0100

AC:

AN:

3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.65

(source)

DANN

Benign

0.56

PhyloP100

-4.9

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