dbSNP rs961831: ENSG00000299280:n.141-21964T>G (chr9-22362105-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000762200.1(ENSG00000299280):n.141-21964T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,194 control chromosomes in the GnomAD database, including 935 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 0.10 ( 935 hom., cov: 32)

Consequence

ENSG00000299280
ENST00000762200.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.680

Publications

14 publications found

Variant links:

Genes affected

ENSG00000299280 (HGNC:):

ENSG00000299280 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=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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
ENSG00000299280	ENST00000762200.1 link	n.141-21964T>G		intron_variant	Intron 2 of 2
ENSG00000299280	ENST00000762202.1 link	n.470+4341T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15492

AN:

152076

Hom.:

932

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.0495

Gnomad AMR

AF:

0.0759

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.0225

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0595

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0860

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.102

AC:

15510

AN:

152194

Hom.:

935

Cov.:

AF XY:

0.101

AC XY:

7501

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.163

AC:

6783

AN:

41504

American (AMR)

AF:

0.0758

AC:

1160

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3470

East Asian (EAS)

AF:

0.0226

AC:

117

AN:

5180

South Asian (SAS)

AF:

0.103

AC:

498

AN:

4816

European-Finnish (FIN)

AF:

0.0595

AC:

631

AN:

10604

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0860

AC:

5849

AN:

68006

Other (OTH)

AF:

0.105

AC:

222

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

707

1414

2121

2828

3535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.0901

Hom.:

2583

Bravo

AF:

0.103

Asia WGS

AF:

0.100

AC:

348

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.7

(source)

DANN

Benign

0.82

PhyloP100

-0.68

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