Genetic Variant ENSG00000303377:n.116-4413C>T (chr10-120283977-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 ENST00000794040.1(ENSG00000303377):n.116-4413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 151,828 control chromosomes in the GnomAD database, including 217 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 0.020 ( 217 hom., cov: 32)

Consequence

ENSG00000303377
ENST00000794040.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

3 publications found

Variant links:

Genes affected

ENSG00000303377 (HGNC:):

ENSG00000303377 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378515	XR_001747605.1 link	n.625-4413C>T		intron_variant	Intron 5 of 6
LOC105378515	XR_001747606.1 link	n.916-4413C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303377	ENST00000794040.1 link	n.116-4413C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0202

AC:

3067

AN:

151712

Hom.:

212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00218

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.0741

Gnomad FIN

AF:

0.00850

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00296

Gnomad OTH

AF:

0.0197

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

GnomAD4 genome

AF:

0.0203

AC:

3083

AN:

151828

Hom.:

217

Cov.:

AF XY:

0.0240

AC XY:

1778

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.00217

AC:

AN:

41410

American (AMR)

AF:

0.0702

AC:

1073

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00778

AC:

AN:

3470

East Asian (EAS)

AF:

0.227

AC:

1174

AN:

5168

South Asian (SAS)

AF:

0.0737

AC:

355

AN:

4814

European-Finnish (FIN)

AF:

0.00850

AC:

AN:

10468

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00296

AC:

201

AN:

67906

Other (OTH)

AF:

0.0247

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

139

278

418

557

696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0119

Hom.:

Bravo

AF:

0.0259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.13

(source)

DANN

Benign

0.50

PhyloP100

-1.4

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