dbSNP rs3037354: ENSG00000297196:n.626_627delCA (chr7-24283306-CTG-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000746097.1(ENSG00000297196):n.626_627delCA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6174 hom., cov: 19)

Consequence

ENSG00000297196
ENST00000746097.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796

Publications

14 publications found

Variant links:

Genes affected

ENSG00000297196 (HGNC:):

ENSG00000297196 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107986777	XR_001745121.2 link	n.209+36049_209+36050delCA	intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2 link	n.81-86279_81-86278delCA	intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2 link	n.209+36049_209+36050delCA	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297196	ENST00000746097.1 link	n.626_627delCA	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297196	ENST00000746098.1 link	n.681_682delCA	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000228944	ENST00000718234.1 link	n.319+36049_319+36050delCA	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42663

AN:

151926

Hom.:

6166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.285

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

GnomAD4 genome

AF:

0.281

AC:

42692

AN:

152044

Hom.:

6174

Cov.:

AF XY:

0.280

AC XY:

20794

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.343

AC:

14230

AN:

41460

American (AMR)

AF:

0.223

AC:

3407

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

850

AN:

3468

East Asian (EAS)

AF:

0.309

AC:

1598

AN:

5178

South Asian (SAS)

AF:

0.298

AC:

1433

AN:

4812

European-Finnish (FIN)

AF:

0.251

AC:

2653

AN:

10562

Middle Eastern (MID)

AF:

0.315

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.257

AC:

17463

AN:

67954

Other (OTH)

AF:

0.285

AC:

601

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1571

3141

4712

6282

7853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.268

Hom.:

710

Bravo

AF:

0.281

Asia WGS

AF:

0.310

AC:

1076

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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