dbSNP rs10895454: ENSG00000307600:n.218+1113G>T (chr11-103528964-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000827359.1(ENSG00000307600):n.218+1113G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,142 control chromosomes in the GnomAD database, including 13,732 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 0.40 ( 13732 hom., cov: 33)

Consequence

ENSG00000307600
ENST00000827359.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.563

Publications

4 publications found

Variant links:

Genes affected

ENSG00000307600 (HGNC:):

ENSG00000307600 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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307600	ENST00000827359.1 link	n.218+1113G>T	intron_variant	Intron 2 of 2
ENSG00000307600	ENST00000827360.1 link	n.92+7445G>T	intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827361.1 link	n.105+1113G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60589

AN:

152024

Hom.:

13732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.414

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.481

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.417

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

GnomAD4 genome

AF:

0.398

AC:

60595

AN:

152142

Hom.:

13732

Cov.:

AF XY:

0.393

AC XY:

29228

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.197

AC:

8191

AN:

41522

American (AMR)

AF:

0.366

AC:

5590

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.495

AC:

1717

AN:

3468

East Asian (EAS)

AF:

0.220

AC:

1142

AN:

5182

South Asian (SAS)

AF:

0.353

AC:

1703

AN:

4830

European-Finnish (FIN)

AF:

0.481

AC:

5076

AN:

10558

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.526

AC:

35764

AN:

67976

Other (OTH)

AF:

0.413

AC:

873

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1741

3482

5223

6964

8705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.337

Hom.:

1454

Bravo

AF:

0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.0

(source)

DANN

Benign

0.48

PhyloP100

0.56

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