dbSNP rs10519957: ENSG00000248799:n.194+5572C>T (chr5-127697155-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000827053.1(ENSG00000248799):n.194+5572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 151,822 control chromosomes in the GnomAD database, including 571 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 0.058 ( 571 hom., cov: 32)

Consequence

ENSG00000248799
ENST00000827053.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.484

Publications

1 publications found

Variant links:

Genes affected

ENSG00000248799 (HGNC:):

ENSG00000248799 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000248799	ENST00000827053.1 link	n.194+5572C>T	intron_variant	Intron 1 of 3
ENSG00000248799	ENST00000827054.1 link	n.198+12141C>T	intron_variant	Intron 2 of 2
ENSG00000248799	ENST00000827055.1 link	n.252+5572C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0577

AC:

8754

AN:

151704

Hom.:

570

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0913

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.0906

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.0817

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0106

Gnomad OTH

AF:

0.0686

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

GnomAD4 genome

AF:

0.0578

AC:

8768

AN:

151822

Hom.:

571

Cov.:

AF XY:

0.0608

AC XY:

4510

AN XY:

74194

show subpopulations

African (AFR)

AF:

0.0913

AC:

3779

AN:

41398

American (AMR)

AF:

0.131

AC:

1987

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.0906

AC:

314

AN:

3464

East Asian (EAS)

AF:

0.268

AC:

1379

AN:

5148

South Asian (SAS)

AF:

0.0820

AC:

393

AN:

4794

European-Finnish (FIN)

AF:

0.00104

AC:

AN:

10560

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0106

AC:

719

AN:

67926

Other (OTH)

AF:

0.0717

AC:

151

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

377

753

1130

1506

1883

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0356

Hom.:

Bravo

AF:

0.0703

Asia WGS

AF:

0.170

AC:

591

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.58

(source)

DANN

Benign

0.80

PhyloP100

-0.48

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