Genetic Variant ENSG00000303916:n.161-4563C>T (chr21-15150025-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 ENST00000798068.1(ENSG00000303916):n.161-4563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,890 control chromosomes in the GnomAD database, including 1,543 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 ( 1543 hom., cov: 32)

Consequence

ENSG00000303916
ENST00000798068.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

2 publications found

Variant links:

Genes affected

ENSG00000303916 (HGNC:):

ENSG00000303916 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303916	ENST00000798068.1 link	n.161-4563C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17708

AN:

151772

Hom.:

1541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0838

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.00213

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.0223

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0784

Gnomad OTH

AF:

0.128

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

GnomAD4 genome

AF:

0.117

AC:

17725

AN:

151890

Hom.:

1543

Cov.:

AF XY:

0.111

AC XY:

8257

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.238

AC:

9843

AN:

41364

American (AMR)

AF:

0.0837

AC:

1277

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

393

AN:

3468

East Asian (EAS)

AF:

0.00213

AC:

AN:

5154

South Asian (SAS)

AF:

0.0435

AC:

209

AN:

4802

European-Finnish (FIN)

AF:

0.0223

AC:

236

AN:

10564

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0784

AC:

5331

AN:

67968

Other (OTH)

AF:

0.127

AC:

268

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

731

1462

2193

2924

3655

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0754

Hom.:

411

Bravo

AF:

0.129

Asia WGS

AF:

0.0330

AC:

118

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.15

(source)

DANN

Benign

0.26

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