dbSNP rs10510322: ENSG00000229642:n.1010+36127C>T (chr3-5999642-C-T) – 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.1010+36127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 152,170 control chromosomes in the GnomAD database, including 1,323 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 0.078 ( 1323 hom., cov: 32)

Consequence

ENSG00000229642
ENST00000425894.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.204

Publications

1 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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.1010+36127C>T	intron_variant	Intron 6 of 8	3
ENSG00000229642	ENST00000779001.1 link	n.1157+36127C>T	intron_variant	Intron 6 of 7
ENSG00000229642	ENST00000779002.1 link	n.781+36127C>T	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.0780

AC:

11863

AN:

152052

Hom.:

1324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0409

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00416

Gnomad OTH

AF:

0.0576

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

GnomAD4 genome

AF:

0.0781

AC:

11884

AN:

152170

Hom.:

1323

Cov.:

AF XY:

0.0766

AC XY:

5702

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.247

AC:

10238

AN:

41476

American (AMR)

AF:

0.0408

AC:

624

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

AN:

3466

East Asian (EAS)

AF:

0.00367

AC:

AN:

5178

South Asian (SAS)

AF:

0.109

AC:

525

AN:

4820

European-Finnish (FIN)

AF:

0.000377

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00416

AC:

283

AN:

68014

Other (OTH)

AF:

0.0565

AC:

119

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

475

949

1424

1898

2373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

122

244

366

488

610

<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:

0.0457

Hom.:

106

Bravo

AF:

0.0858

Asia WGS

AF:

0.0750

AC:

265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.9

(source)

DANN

Benign

0.61

PhyloP100

0.20

Mutation Taster

=100/0

polymorphism

(source)

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