dbSNP rs9321063: ENSG00000271860:n.648-1891A>G (chr6-98448791-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000847792.1(ENSG00000271860):n.648-1891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,172 control chromosomes in the GnomAD database, including 413 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 0.069 ( 413 hom., cov: 33)

Consequence

ENSG00000271860
ENST00000847792.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.456

Publications

4 publications found

Variant links:

Genes affected

ENSG00000271860 (HGNC:):

ENSG00000271860 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000271860	ENST00000847792.1 link	n.648-1891A>G	intron_variant	Intron 6 of 7
ENSG00000271860	ENST00000847793.1 link	n.612-1891A>G	intron_variant	Intron 6 of 9
ENSG00000271860	ENST00000847794.1 link	n.461-13532A>G	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0694

AC:

10548

AN:

152054

Hom.:

412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0753

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.00737

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.0753

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.0599

Gnomad OTH

AF:

0.0608

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

GnomAD4 genome

AF:

0.0695

AC:

10569

AN:

152172

Hom.:

413

Cov.:

AF XY:

0.0705

AC XY:

5243

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.102

AC:

4232

AN:

41548

American (AMR)

AF:

0.0752

AC:

1149

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3472

East Asian (EAS)

AF:

0.00719

AC:

AN:

5146

South Asian (SAS)

AF:

0.0112

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0753

AC:

799

AN:

10606

Middle Eastern (MID)

AF:

0.0411

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0599

AC:

4073

AN:

67988

Other (OTH)

AF:

0.0601

AC:

127

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

498

996

1495

1993

2491

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0599

Hom.:

530

Bravo

AF:

0.0717

Asia WGS

AF:

0.0390

AC:

136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.62

(source)

DANN

Benign

0.17

PhyloP100

-0.46

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