dbSNP rs10283761: ENSG00000254261:n.354+7620T>C (chr9-26755932-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000523363.2(ENSG00000254261):n.354+7620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,122 control chromosomes in the GnomAD database, including 5,838 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 0.24 ( 5838 hom., cov: 33)

Consequence

ENSG00000254261
ENST00000523363.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.712

Publications

1 publications found

Variant links:

Genes affected

ENSG00000254261 (HGNC:):

ENSG00000254261 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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
ENSG00000254261	ENST00000523363.2 link	n.354+7620T>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35777

AN:

152004

Hom.:

5825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.0720

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.236

AC:

35830

AN:

152122

Hom.:

5838

Cov.:

AF XY:

0.235

AC XY:

17475

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.455

AC:

18837

AN:

41432

American (AMR)

AF:

0.160

AC:

2451

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

520

AN:

3472

East Asian (EAS)

AF:

0.0717

AC:

372

AN:

5186

South Asian (SAS)

AF:

0.350

AC:

1686

AN:

4820

European-Finnish (FIN)

AF:

0.135

AC:

1433

AN:

10588

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.145

AC:

9864

AN:

68006

Other (OTH)

AF:

0.212

AC:

448

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1265

2529

3794

5058

6323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.164

Hom.:

3729

Bravo

AF:

0.240

Asia WGS

AF:

0.226

AC:

788

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.6

(source)

DANN

Benign

0.79

PhyloP100

0.71

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