dbSNP rs12667374: ENSG00000225718:n.591-12178C>T (chr7-69236985-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 ENST00000435148.1(ENSG00000225718):n.591-12178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 152,294 control chromosomes in the GnomAD database, including 109 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 0.031 ( 109 hom., cov: 32)

Consequence

ENSG00000225718
ENST00000435148.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.449

Publications

3 publications found

Variant links:

Genes affected

ENSG00000225718 (HGNC:):

ENSG00000225718 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000225718	ENST00000435148.1 link	n.591-12178C>T	intron_variant	Intron 2 of 2	3
ENSG00000225718	ENST00000670444.1 link	n.530+34980C>T	intron_variant	Intron 2 of 2
ENSG00000225718	ENST00000716162.1 link	n.493-24142C>T	intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes

AF:

0.0311

AC:

4736

AN:

152176

Hom.:

110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00960

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0315

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.0618

Gnomad SAS

AF:

0.00892

Gnomad FIN

AF:

0.0208

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0467

Gnomad OTH

AF:

0.0296

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

GnomAD4 genome

AF:

0.0311

AC:

4733

AN:

152294

Hom.:

109

Cov.:

AF XY:

0.0292

AC XY:

2177

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00957

AC:

398

AN:

41570

American (AMR)

AF:

0.0314

AC:

480

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00922

AC:

AN:

3472

East Asian (EAS)

AF:

0.0621

AC:

322

AN:

5184

South Asian (SAS)

AF:

0.00851

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0208

AC:

221

AN:

10602

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0466

AC:

3173

AN:

68030

Other (OTH)

AF:

0.0298

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

247

495

742

990

1237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0362

Hom.:

117

Bravo

AF:

0.0325

Asia WGS

AF:

0.0370

AC:

128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.3

(source)

DANN

Benign

0.53

PhyloP100

0.45

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