dbSNP rs1956932: ENSG00000258744:n.375-2946A>G (chr14-24498614-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000555109.2(ENSG00000258744):n.375-2946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 152,182 control chromosomes in the GnomAD database, including 657 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 0.087 ( 657 hom., cov: 32)

Consequence

ENSG00000258744
ENST00000555109.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

8 publications found

Variant links:

Genes affected

ENSG00000258744 (HGNC:):

ENSG00000258744 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927045	NR_110032.1 link	n.1479-2946A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000258744	ENST00000555109.2 link	n.375-2946A>G	intron_variant	Intron 2 of 3	5
ENSG00000258744	ENST00000656888.2 link	n.304-2946A>G	intron_variant	Intron 2 of 2
ENSG00000258744	ENST00000816252.1 link	n.263-2946A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0871

AC:

13244

AN:

152064

Hom.:

656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0519

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0722

Gnomad ASJ

AF:

0.0634

Gnomad EAS

AF:

0.0113

Gnomad SAS

AF:

0.0825

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.0990

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

GnomAD4 genome

AF:

0.0870

AC:

13246

AN:

152182

Hom.:

657

Cov.:

AF XY:

0.0857

AC XY:

6377

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0518

AC:

2153

AN:

41530

American (AMR)

AF:

0.0720

AC:

1100

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0634

AC:

220

AN:

3472

East Asian (EAS)

AF:

0.0114

AC:

AN:

5188

South Asian (SAS)

AF:

0.0840

AC:

405

AN:

4820

European-Finnish (FIN)

AF:

0.117

AC:

1245

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.114

AC:

7742

AN:

67974

Other (OTH)

AF:

0.0975

AC:

206

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

606

1211

1817

2422

3028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.106

Hom.:

1580

Bravo

AF:

0.0821

Asia WGS

AF:

0.0470

AC:

163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.78

(source)

DANN

Benign

0.68

PhyloP100

-1.1

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