dbSNP rs17564315: ENSG00000305355:n.236-14529C>T (chr2-19758735-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 ENST00000810569.1(ENSG00000305355):n.236-14529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,234 control chromosomes in the GnomAD database, including 1,737 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 0.15 ( 1737 hom., cov: 33)

Consequence

ENSG00000305355
ENST00000810569.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

Publications

7 publications found

Variant links:

Genes affected

ENSG00000305355 (HGNC:):

ENSG00000305355 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 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
ENSG00000305355	ENST00000810569.1 link	n.236-14529C>T		intron_variant	Intron 2 of 2
ENSG00000305355	ENST00000810570.1 link	n.222-8156C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22318

AN:

152116

Hom.:

1729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0937

Gnomad EAS

AF:

0.0828

Gnomad SAS

AF:

0.0656

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.146

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

GnomAD4 genome

AF:

0.147

AC:

22357

AN:

152234

Hom.:

1737

Cov.:

AF XY:

0.143

AC XY:

10620

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.137

AC:

5696

AN:

41552

American (AMR)

AF:

0.142

AC:

2179

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0937

AC:

325

AN:

3470

East Asian (EAS)

AF:

0.0836

AC:

432

AN:

5170

South Asian (SAS)

AF:

0.0659

AC:

318

AN:

4828

European-Finnish (FIN)

AF:

0.151

AC:

1598

AN:

10598

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11412

AN:

67996

Other (OTH)

AF:

0.149

AC:

314

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

983

1966

2948

3931

4914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.161

Hom.:

6035

Bravo

AF:

0.147

Asia WGS

AF:

0.109

AC:

379

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

1.4

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