Genetic Variant ENST00000846710.1:n.329-3217_329-3216insA (chr22-46144361-A-AT) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000846710.1(ENSG00000310037):n.329-3217_329-3216insA variant causes a intron 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 0.29 ( 6360 hom., cov: 0)

Consequence

ENSG00000310037
ENST00000846710.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259

Publications

1 publications found

Variant links:

Genes affected

ENSG00000310037 (HGNC:):

ENSG00000310037 links:

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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 = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310037	ENST00000846710.1		n.329-3217_329-3216insA		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.311+1389_311+1390insA		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

42356

AN:

143966

Hom.:

6354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.0850

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.227

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.299

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

GnomAD4 genome

AF:

0.294

AC:

42390

AN:

144014

Hom.:

6360

Cov.:

AF XY:

0.288

AC XY:

20077

AN XY:

69730

show subpopulations

African (AFR)

AF:

0.342

AC:

13413

AN:

39206

American (AMR)

AF:

0.216

AC:

3119

AN:

14432

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

771

AN:

3368

East Asian (EAS)

AF:

0.0851

AC:

414

AN:

4864

South Asian (SAS)

AF:

0.210

AC:

937

AN:

4452

European-Finnish (FIN)

AF:

0.265

AC:

2371

AN:

8934

Middle Eastern (MID)

AF:

0.232

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.309

AC:

20301

AN:

65630

Other (OTH)

AF:

0.297

AC:

584

AN:

1966

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1350

2700

4051

5401

6751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.160

Hom.:

318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.26

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over