dbSNP rs445942: ENSG00000302889:n.644+475T>C (chr7-41299906-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 ENST00000790257.1(ENSG00000302889):n.644+475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 152,322 control chromosomes in the GnomAD database, including 332 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 0.039 ( 332 hom., cov: 32)

Consequence

ENSG00000302889
ENST00000790257.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.947

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302889 (HGNC:):

ENSG00000302889 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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
ENSG00000302889	ENST00000790257.1 link	n.644+475T>C		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.0385

AC:

5859

AN:

152204

Hom.:

329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0227

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00101

Gnomad OTH

AF:

0.0335

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

GnomAD4 genome

AF:

0.0387

AC:

5893

AN:

152322

Hom.:

332

Cov.:

AF XY:

0.0400

AC XY:

2980

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.104

AC:

4335

AN:

41552

American (AMR)

AF:

0.0210

AC:

322

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00288

AC:

AN:

3470

East Asian (EAS)

AF:

0.187

AC:

971

AN:

5182

South Asian (SAS)

AF:

0.0228

AC:

110

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00101

AC:

AN:

68030

Other (OTH)

AF:

0.0326

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

268

536

805

1073

1341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0260

Hom.:

126

Bravo

AF:

0.0443

Asia WGS

AF:

0.0760

AC:

264

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.34

(source)

DANN

Benign

0.54

PhyloP100

-0.95

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