dbSNP rs1006559: ENSG00000267320:n.277-8135A>T (chr19-28345879-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000587140.5(ENSG00000267320):n.277-8135A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,202 control chromosomes in the GnomAD database, including 695 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 0.062 ( 695 hom., cov: 32)

Consequence

ENSG00000267320
ENST00000587140.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215

Publications

1 publications found

Variant links:

Genes affected

ENSG00000267320 (HGNC:):

ENSG00000267320 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 (EAS) allele frequency at 95% confidence interval = 0.234 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
ENSG00000267320	ENST00000587140.5 link	n.277-8135A>T		intron_variant	Intron 3 of 4	5
ENSG00000267320	ENST00000592311.5 link	n.251-25621A>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.0619

AC:

9412

AN:

152084

Hom.:

686

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.0302

Gnomad FIN

AF:

0.00989

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00354

Gnomad OTH

AF:

0.0550

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

GnomAD4 genome

AF:

0.0621

AC:

9449

AN:

152202

Hom.:

695

Cov.:

AF XY:

0.0637

AC XY:

4740

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.131

AC:

5447

AN:

41500

American (AMR)

AF:

0.137

AC:

2097

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00807

AC:

AN:

3468

East Asian (EAS)

AF:

0.245

AC:

1265

AN:

5162

South Asian (SAS)

AF:

0.0299

AC:

144

AN:

4824

European-Finnish (FIN)

AF:

0.00989

AC:

105

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00354

AC:

241

AN:

68020

Other (OTH)

AF:

0.0539

AC:

114

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

404

809

1213

1618

2022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0356

Hom.:

Bravo

AF:

0.0773

Asia WGS

AF:

0.149

AC:

518

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

5.0

(source)

DANN

Benign

0.65

PhyloP100

0.21

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