dbSNP rs35598594: ENSG00000300853:n.169+2113dupT (chr8-27594724-G-GT) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000774578.1(ENSG00000300853):n.169+2113dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,188 control chromosomes in the GnomAD database, including 1,163 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1163 hom., cov: 30)

Consequence

ENSG00000300853
ENST00000774578.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.478

Publications

1 publications found

Variant links:

Genes affected

ENSG00000300853 (HGNC:):

ENSG00000300853 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 (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901919	XR_007060868.1 link	n.1397+2113dupT		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300853	ENST00000774578.1 link	n.169+2113dupT	intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774579.1 link	n.284+1426dupT	intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774580.1 link	n.128+1467dupT	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16279

AN:

152070

Hom.:

1163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0279

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0920

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.107

AC:

16285

AN:

152188

Hom.:

1163

Cov.:

AF XY:

0.104

AC XY:

7727

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.0278

AC:

1157

AN:

41550

American (AMR)

AF:

0.100

AC:

1533

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

615

AN:

3468

East Asian (EAS)

AF:

0.000965

AC:

AN:

5184

South Asian (SAS)

AF:

0.0929

AC:

448

AN:

4820

European-Finnish (FIN)

AF:

0.123

AC:

1300

AN:

10576

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10860

AN:

67986

Other (OTH)

AF:

0.120

AC:

253

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

712

1423

2135

2846

3558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.132

Hom.:

189

Bravo

AF:

0.101

Asia WGS

AF:

0.0370

AC:

128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.48

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