Genetic Variant ENSG00000248783:n.471+63612G>A (chr5-12466863-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 ENST00000830573.1(ENSG00000248783):n.471+63612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 152,216 control chromosomes in the GnomAD database, including 164 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 0.038 ( 164 hom., cov: 32)

Consequence

ENSG00000248783
ENST00000830573.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.13

Publications

3 publications found

Variant links:

Genes affected

ENSG00000248783 (HGNC:):

ENSG00000248783 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374655	NR_188266.1 link	n.365+63612G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000248783	ENST00000830573.1 link	n.471+63612G>A	intron_variant	Intron 3 of 5
ENSG00000248783	ENST00000830574.1 link	n.490+63612G>A	intron_variant	Intron 3 of 4
ENSG00000248783	ENST00000830575.1 link	n.490+63612G>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0380

AC:

5774

AN:

152098

Hom.:

162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0646

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0335

Gnomad ASJ

AF:

0.0553

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0514

Gnomad FIN

AF:

0.00650

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0288

Gnomad OTH

AF:

0.0383

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

GnomAD4 genome

AF:

0.0380

AC:

5785

AN:

152216

Hom.:

164

Cov.:

AF XY:

0.0374

AC XY:

2781

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0647

AC:

2689

AN:

41530

American (AMR)

AF:

0.0334

AC:

511

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0553

AC:

192

AN:

3472

East Asian (EAS)

AF:

0.000581

AC:

AN:

5164

South Asian (SAS)

AF:

0.0517

AC:

249

AN:

4820

European-Finnish (FIN)

AF:

0.00650

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0288

AC:

1959

AN:

68014

Other (OTH)

AF:

0.0379

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

273

546

818

1091

1364

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0369

Hom.:

Bravo

AF:

0.0410

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.044

(source)

DANN

Benign

0.82

PhyloP100

-3.1

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