dbSNP rs2900032: ENSG00000258751:n.123+22917A>G (chr14-48468728-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000555693.1(ENSG00000258751):n.123+22917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 151,526 control chromosomes in the GnomAD database, including 351 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 0.063 ( 351 hom., cov: 32)

Consequence

ENSG00000258751
ENST00000555693.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.145

Publications

1 publications found

Variant links:

Genes affected

ENSG00000258751 (HGNC:):

ENSG00000258751 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 (NFE) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1 link	n.426-39485A>G		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258751	ENST00000555693.1 link	n.123+22917A>G		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.0630

AC:

9536

AN:

151408

Hom.:

351

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0449

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0565

Gnomad FIN

AF:

0.0925

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.0737

Gnomad OTH

AF:

0.0720

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

GnomAD4 genome

AF:

0.0629

AC:

9537

AN:

151526

Hom.:

351

Cov.:

AF XY:

0.0624

AC XY:

4622

AN XY:

74074

show subpopulations

African (AFR)

AF:

0.0448

AC:

1839

AN:

41020

American (AMR)

AF:

0.0503

AC:

765

AN:

15204

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

419

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.0567

AC:

274

AN:

4830

European-Finnish (FIN)

AF:

0.0925

AC:

977

AN:

10562

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0737

AC:

5007

AN:

67946

Other (OTH)

AF:

0.0712

AC:

150

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

458

917

1375

1834

2292

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0647

Hom.:

Bravo

AF:

0.0582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.6

(source)

DANN

Benign

0.72

PhyloP100

0.14

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