dbSNP rs140759: ENSG00000308468:n.95-60257_95-60254delAAAG (chr6-120068309-CAAAG-C) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000834274.1(ENSG00000308468):n.95-60257_95-60254delAAAG 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 0.31 ( 7740 hom., cov: 0)

Consequence

ENSG00000308468
ENST00000834274.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Publications

2 publications found

Variant links:

Genes affected

ENSG00000308468 (HGNC:):

ENSG00000308468 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 (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308468	ENST00000834274.1		n.95-60257_95-60254delAAAG		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47350

AN:

150794

Hom.:

7734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.280

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.302

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

GnomAD4 genome

AF:

0.314

AC:

47365

AN:

150912

Hom.:

7740

Cov.:

AF XY:

0.309

AC XY:

22758

AN XY:

73762

show subpopulations

African (AFR)

AF:

0.254

AC:

10524

AN:

41356

American (AMR)

AF:

0.364

AC:

5507

AN:

15126

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

1187

AN:

3438

East Asian (EAS)

AF:

0.236

AC:

1216

AN:

5154

South Asian (SAS)

AF:

0.279

AC:

1340

AN:

4810

European-Finnish (FIN)

AF:

0.231

AC:

2421

AN:

10492

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.357

AC:

23972

AN:

67240

Other (OTH)

AF:

0.299

AC:

627

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1653

3306

4959

6612

8265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.342

Hom.:

1050

Bravo

AF:

0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

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