dbSNP rs10969156: ENSG00000300910:n.254+11470T>G (chr9-29438919-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000775037.1(ENSG00000300910):n.254+11470T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 152,028 control chromosomes in the GnomAD database, including 121 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 0.034 ( 121 hom., cov: 32)

Consequence

ENSG00000300910
ENST00000775037.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0770

Publications

0 publications found

Variant links:

COSMIC-nc: COSV69457094

Genes affected

ENSG00000300910 (HGNC:):

ENSG00000300910 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0804 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
ENSG00000300910	ENST00000775037.1 link	n.254+11470T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0344

AC:

5227

AN:

151910

Hom.:

118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0327

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.0292

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.0872

Gnomad SAS

AF:

0.0266

Gnomad FIN

AF:

0.0221

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.0342

Gnomad OTH

AF:

0.0301

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

GnomAD4 genome

AF:

0.0344

AC:

5237

AN:

152028

Hom.:

121

Cov.:

AF XY:

0.0337

AC XY:

2503

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.0328

AC:

1362

AN:

41496

American (AMR)

AF:

0.0293

AC:

447

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0251

AC:

AN:

3470

East Asian (EAS)

AF:

0.0871

AC:

445

AN:

5112

South Asian (SAS)

AF:

0.0271

AC:

130

AN:

4800

European-Finnish (FIN)

AF:

0.0221

AC:

234

AN:

10570

Middle Eastern (MID)

AF:

0.0377

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0342

AC:

2325

AN:

67988

Other (OTH)

AF:

0.0298

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

245

489

734

978

1223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0338

Hom.:

Bravo

AF:

0.0372

Asia WGS

AF:

0.0460

AC:

159

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

(source)

DANN

Benign

0.71

PhyloP100

-0.077

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