dbSNP rs2169520: ENSG00000307084:n.286+582T>C (chr5-63302626-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000823418.1(ENSG00000307084):n.286+582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,086 control chromosomes in the GnomAD database, including 5,260 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 0.24 ( 5260 hom., cov: 32)

Consequence

ENSG00000307084
ENST00000823418.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.417

Publications

6 publications found

Variant links:

Genes affected

ENSG00000307084 (HGNC:):

ENSG00000307084 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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
ENSG00000307084	ENST00000823418.1 link	n.286+582T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37157

AN:

151968

Hom.:

5250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.265

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

GnomAD4 genome

AF:

0.245

AC:

37190

AN:

152086

Hom.:

5260

Cov.:

AF XY:

0.236

AC XY:

17542

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.387

AC:

16061

AN:

41448

American (AMR)

AF:

0.212

AC:

3236

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

777

AN:

3470

East Asian (EAS)

AF:

0.138

AC:

714

AN:

5178

South Asian (SAS)

AF:

0.101

AC:

487

AN:

4826

European-Finnish (FIN)

AF:

0.102

AC:

1077

AN:

10606

Middle Eastern (MID)

AF:

0.397

AC:

116

AN:

292

European-Non Finnish (NFE)

AF:

0.206

AC:

14010

AN:

67988

Other (OTH)

AF:

0.264

AC:

557

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1369

2739

4108

5478

6847

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.223

Hom.:

6712

Bravo

AF:

0.264

Asia WGS

AF:

0.130

AC:

455

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

7.3

(source)

DANN

Benign

0.78

PhyloP100

-0.42

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