dbSNP rs1910003: ENSG00000248752:n.471+8666C>T (chr5-125968854-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 ENST00000651847.1(ENSG00000248752):n.471+8666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,940 control chromosomes in the GnomAD database, including 1,121 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 ( 1121 hom., cov: 32)

Consequence

ENSG00000248752
ENST00000651847.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.466

Publications

2 publications found

Variant links:

COSMIC-nc: COSV72115551

Genes affected

ENSG00000248752 (HGNC:):

ENSG00000248752 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1 link	n.1774+129153C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000651847.1 link	n.471+8666C>T		intron_variant	Intron 5 of 15

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18256

AN:

151822

Hom.:

1120

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0802

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.120

AC:

18269

AN:

151940

Hom.:

1121

Cov.:

AF XY:

0.119

AC XY:

8872

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.133

AC:

5508

AN:

41478

American (AMR)

AF:

0.0801

AC:

1222

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

383

AN:

3468

East Asian (EAS)

AF:

0.110

AC:

561

AN:

5104

South Asian (SAS)

AF:

0.133

AC:

641

AN:

4814

European-Finnish (FIN)

AF:

0.120

AC:

1264

AN:

10572

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8314

AN:

67934

Other (OTH)

AF:

0.114

AC:

242

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

826

1652

2479

3305

4131

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.120

Hom.:

4978

Bravo

AF:

0.117

Asia WGS

AF:

0.104

AC:

361

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

8.2

(source)

DANN

Benign

0.38

PhyloP100

0.47

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