dbSNP rs748192: ENSG00000229642:n.571+6350T>A (chr3-5847593-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425894.2(ENSG00000229642):n.571+6350T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,094 control chromosomes in the GnomAD database, including 1,853 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 0.15 ( 1853 hom., cov: 31)

Consequence

ENSG00000229642
ENST00000425894.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

3 publications found

Variant links:

Genes affected

ENSG00000229642 (HGNC:):

ENSG00000229642 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 (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000229642	ENST00000425894.2 link	n.571+6350T>A	intron_variant	Intron 4 of 8	3
ENSG00000229642	ENST00000779001.1 link	n.322+6350T>A	intron_variant	Intron 3 of 7
ENSG00000229642	ENST00000779002.1 link	n.342+6350T>A	intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22319

AN:

151978

Hom.:

1854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0905

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.147

AC:

22329

AN:

152094

Hom.:

1853

Cov.:

AF XY:

0.148

AC XY:

11024

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0904

AC:

3753

AN:

41500

American (AMR)

AF:

0.224

AC:

3430

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

570

AN:

3470

East Asian (EAS)

AF:

0.139

AC:

718

AN:

5158

South Asian (SAS)

AF:

0.112

AC:

539

AN:

4810

European-Finnish (FIN)

AF:

0.165

AC:

1746

AN:

10590

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10945

AN:

67972

Other (OTH)

AF:

0.175

AC:

368

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

958

1915

2873

3830

4788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.149

Hom.:

187

Bravo

AF:

0.149

Asia WGS

AF:

0.113

AC:

392

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.90

(source)

DANN

Benign

0.48

PhyloP100

-1.7

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