dbSNP rs9470361: ENSG00000301446:n.192+5079C>T (chr6-36655602-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000778909.1(ENSG00000301446):n.192+5079C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,114 control chromosomes in the GnomAD database, including 5,420 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5420 hom., cov: 32)

Consequence

ENSG00000301446
ENST00000778909.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Publications

44 publications found

Variant links:

Genes affected

ENSG00000301446 (HGNC:):

ENSG00000301446 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301446	ENST00000778909.1 link	n.192+5079C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39921

AN:

151996

Hom.:

5409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.294

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

GnomAD4 genome

AF:

0.263

AC:

39952

AN:

152114

Hom.:

5420

Cov.:

AF XY:

0.259

AC XY:

19269

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.323

AC:

13411

AN:

41498

American (AMR)

AF:

0.227

AC:

3473

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1240

AN:

3468

East Asian (EAS)

AF:

0.170

AC:

881

AN:

5176

South Asian (SAS)

AF:

0.322

AC:

1553

AN:

4816

European-Finnish (FIN)

AF:

0.192

AC:

2031

AN:

10574

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.243

AC:

16501

AN:

67986

Other (OTH)

AF:

0.300

AC:

634

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1530

3061

4591

6122

7652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.247

Hom.:

16357

Bravo

AF:

0.263

Asia WGS

AF:

0.286

AC:

995

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.6

(source)

DANN

Benign

0.41

PhyloP100

0.15

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