dbSNP rs10508743: ENSG00000299869:n.202-11766T>C (chr10-29135369-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 ENST00000766991.1(ENSG00000299869):n.202-11766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,100 control chromosomes in the GnomAD database, including 5,078 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 0.25 ( 5078 hom., cov: 32)

Consequence

ENSG00000299869
ENST00000766991.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284

Publications

6 publications found

Variant links:

Genes affected

ENSG00000299869 (HGNC:):

ENSG00000299869 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299869	ENST00000766991.1 link	n.202-11766T>C	intron_variant	Intron 2 of 2
ENSG00000299869	ENST00000766992.1 link	n.340-301T>C	intron_variant	Intron 3 of 3
ENSG00000299869	ENST00000766993.1 link	n.972-301T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37969

AN:

151984

Hom.:

5064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.218

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

GnomAD4 genome

AF:

0.250

AC:

38001

AN:

152100

Hom.:

5078

Cov.:

AF XY:

0.249

AC XY:

18526

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.176

AC:

7296

AN:

41524

American (AMR)

AF:

0.289

AC:

4411

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

851

AN:

3466

East Asian (EAS)

AF:

0.480

AC:

2474

AN:

5150

South Asian (SAS)

AF:

0.216

AC:

1038

AN:

4814

European-Finnish (FIN)

AF:

0.260

AC:

2753

AN:

10590

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18460

AN:

67976

Other (OTH)

AF:

0.217

AC:

458

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1436

2872

4308

5744

7180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.263

Hom.:

15184

Bravo

AF:

0.252

Asia WGS

AF:

0.325

AC:

1129

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

(source)

DANN

Benign

0.68

PhyloP100

-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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