dbSNP rs1424574: ENSG00000234352:n.656-78395T>C (chr7-136864286-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 ENST00000439694.6(ENSG00000234352):n.656-78395T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,252 control chromosomes in the GnomAD database, including 1,340 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 0.13 ( 1340 hom., cov: 32)

Consequence

ENSG00000234352
ENST00000439694.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.693

Publications

3 publications found

Variant links:

Genes affected

ENSG00000234352 (HGNC:):

ENSG00000234352 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=-0.48).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 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
ENSG00000234352	ENST00000439694.6 link	n.656-78395T>C	intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000586239.5 link	n.274-78395T>C	intron_variant	Intron 2 of 4	5
ENSG00000234352	ENST00000592183.5 link	n.475-78395T>C	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19063

AN:

152134

Hom.:

1341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0789

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0116

Gnomad SAS

AF:

0.0793

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.125

AC:

19053

AN:

152252

Hom.:

1340

Cov.:

AF XY:

0.122

AC XY:

9065

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0787

AC:

3270

AN:

41560

American (AMR)

AF:

0.118

AC:

1798

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

412

AN:

3470

East Asian (EAS)

AF:

0.0114

AC:

AN:

5172

South Asian (SAS)

AF:

0.0785

AC:

379

AN:

4828

European-Finnish (FIN)

AF:

0.145

AC:

1533

AN:

10600

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.165

AC:

11214

AN:

68004

Other (OTH)

AF:

0.123

AC:

261

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

872

1745

2617

3490

4362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.149

Hom.:

5683

Bravo

AF:

0.121

Asia WGS

AF:

0.0430

AC:

149

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.49

PhyloP100

0.69

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