dbSNP rs12668989: ENSG00000298738:n.224-66284A>G (chr7-86032885-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 ENST00000757672.1(ENSG00000298738):n.224-66284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,328 control chromosomes in the GnomAD database, including 1,493 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 0.14 ( 1493 hom., cov: 32)

Consequence

ENSG00000298738
ENST00000757672.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0170

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298738 (HGNC:):

ENSG00000298738 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 (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298738	ENST00000757672.1 link	n.224-66284A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

20890

AN:

151210

Hom.:

1490

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.138

AC:

20894

AN:

151328

Hom.:

1493

Cov.:

AF XY:

0.138

AC XY:

10209

AN XY:

73978

show subpopulations

African (AFR)

AF:

0.115

AC:

4754

AN:

41406

American (AMR)

AF:

0.132

AC:

1989

AN:

15118

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

736

AN:

3456

East Asian (EAS)

AF:

0.154

AC:

785

AN:

5108

South Asian (SAS)

AF:

0.153

AC:

735

AN:

4816

European-Finnish (FIN)

AF:

0.143

AC:

1509

AN:

10576

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.146

AC:

9834

AN:

67536

Other (OTH)

AF:

0.159

AC:

335

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

922

1844

2767

3689

4611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.147

Hom.:

1358

Bravo

AF:

0.140

Asia WGS

AF:

0.146

AC:

507

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.69

PhyloP100

0.017

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