Genetic Variant ENST00000721486.1:n.669+391T>A (chr10-2319919-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000721486.1(ENSG00000294151):n.669+391T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,100 control chromosomes in the GnomAD database, including 1,781 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 0.12 ( 1781 hom., cov: 33)

Consequence

ENSG00000294151
ENST00000721486.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.508

Publications

2 publications found

Variant links:

Genes affected

ENSG00000294151 (HGNC:):

ENSG00000294151 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376349	XR_930551.2 link	n.188+1305T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294151	ENST00000721486.1 link	n.669+391T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17630

AN:

151982

Hom.:

1773

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0919

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0602

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0368

Gnomad OTH

AF:

0.0852

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

GnomAD4 genome

AF:

0.116

AC:

17672

AN:

152100

Hom.:

1781

Cov.:

AF XY:

0.118

AC XY:

8777

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.267

AC:

11073

AN:

41426

American (AMR)

AF:

0.0917

AC:

1401

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

355

AN:

3470

East Asian (EAS)

AF:

0.130

AC:

670

AN:

5170

South Asian (SAS)

AF:

0.160

AC:

770

AN:

4812

European-Finnish (FIN)

AF:

0.0602

AC:

639

AN:

10606

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0368

AC:

2500

AN:

68016

Other (OTH)

AF:

0.0876

AC:

185

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

729

1458

2186

2915

3644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0206

Hom.:

Bravo

AF:

0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.043

(source)

DANN

Benign

0.44

PhyloP100

-0.51

Splicing

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

Publications

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ENST00000721486.1:n.669+391T>A

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