dbSNP rs957646: ENSG00000297645:n.227+12471A>G (chr10-90304565-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 ENST00000749546.1(ENSG00000297645):n.227+12471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,162 control chromosomes in the GnomAD database, including 1,212 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 0.094 ( 1212 hom., cov: 32)

Consequence

ENSG00000297645
ENST00000749546.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.370

Publications

1 publications found

Variant links:

Genes affected

ENSG00000297645 (HGNC:):

ENSG00000297645 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000297645	ENST00000749546.1 link	n.227+12471A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0938

AC:

14256

AN:

152044

Hom.:

1212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0603

Gnomad ASJ

AF:

0.0562

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0213

Gnomad FIN

AF:

0.0270

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0450

Gnomad OTH

AF:

0.0752

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

GnomAD4 genome

AF:

0.0937

AC:

14260

AN:

152162

Hom.:

1212

Cov.:

AF XY:

0.0903

AC XY:

6717

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.229

AC:

9495

AN:

41476

American (AMR)

AF:

0.0602

AC:

920

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0562

AC:

195

AN:

3468

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0211

AC:

102

AN:

4830

European-Finnish (FIN)

AF:

0.0270

AC:

286

AN:

10610

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0450

AC:

3058

AN:

68004

Other (OTH)

AF:

0.0744

AC:

157

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

593

1186

1780

2373

2966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0656

Hom.:

106

Bravo

AF:

0.103

Asia WGS

AF:

0.0250

AC:

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.0

(source)

DANN

Benign

0.76

PhyloP100

-0.37

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