dbSNP rs4646284: ENSG00000301636:n.270dupC (chr6-160160511-T-TG) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000780339.1(ENSG00000301636):n.270dupC 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 0.31 ( 7469 hom., cov: 0)

Consequence

ENSG00000301636
ENST00000780339.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.882

Publications

19 publications found

Variant links:

Genes affected

ENSG00000301636 (HGNC:):

ENSG00000301636 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 = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301636	ENST00000780339.1 link	n.270dupC	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301636	ENST00000780336.1 link	n.370+888dupC	intron_variant	Intron 1 of 1
ENSG00000301636	ENST00000780337.1 link	n.370+888dupC	intron_variant	Intron 1 of 1
ENSG00000301636	ENST00000780338.1 link	n.384-227dupC	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46659

AN:

151976

Hom.:

7448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.399

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.281

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

GnomAD4 genome

AF:

0.307

AC:

46728

AN:

152094

Hom.:

7469

Cov.:

AF XY:

0.300

AC XY:

22317

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.371

AC:

15384

AN:

41468

American (AMR)

AF:

0.264

AC:

4030

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

855

AN:

3468

East Asian (EAS)

AF:

0.297

AC:

1536

AN:

5178

South Asian (SAS)

AF:

0.256

AC:

1231

AN:

4818

European-Finnish (FIN)

AF:

0.237

AC:

2502

AN:

10578

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20187

AN:

67990

Other (OTH)

AF:

0.281

AC:

592

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1657

3315

4972

6630

8287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.299

Hom.:

847

Bravo

AF:

0.308

Asia WGS

AF:

0.289

AC:

1009

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.88

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