dbSNP rs4796870: ENSG00000265554:n.272+3578C>T (chr18-10129079-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000582470.2(ENSG00000265554):n.272+3578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,130 control chromosomes in the GnomAD database, including 2,716 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 0.18 ( 2716 hom., cov: 32)

Consequence

ENSG00000265554
ENST00000582470.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Publications

4 publications found

Variant links:

Genes affected

ENSG00000265554 (HGNC:):

ENSG00000265554 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000265554	ENST00000582470.2 link	n.272+3578C>T	intron_variant	Intron 1 of 1	3
ENSG00000265554	ENST00000669473.1 link	n.422+3578C>T	intron_variant	Intron 2 of 2
ENSG00000265554	ENST00000685786.1 link	n.389-15078C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27760

AN:

152012

Hom.:

2715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.183

AC:

27777

AN:

152130

Hom.:

2716

Cov.:

AF XY:

0.183

AC XY:

13625

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.112

AC:

4661

AN:

41508

American (AMR)

AF:

0.236

AC:

3614

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

565

AN:

3472

East Asian (EAS)

AF:

0.125

AC:

644

AN:

5156

South Asian (SAS)

AF:

0.250

AC:

1203

AN:

4814

European-Finnish (FIN)

AF:

0.222

AC:

2342

AN:

10558

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14210

AN:

68006

Other (OTH)

AF:

0.176

AC:

373

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1174

2348

3523

4697

5871

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.198

Hom.:

3822

Bravo

AF:

0.179

Asia WGS

AF:

0.184

AC:

638

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

(source)

DANN

Benign

0.79

PhyloP100

0.21

Mutation Taster

=100/0

polymorphism

(source)

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