dbSNP rs10969139: ENSG00000300910:n.254+38049A>G (chr9-29412340-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 ENST00000775037.1(ENSG00000300910):n.254+38049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 151,000 control chromosomes in the GnomAD database, including 123 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 0.035 ( 123 hom., cov: 32)

Consequence

ENSG00000300910
ENST00000775037.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.97

Publications

0 publications found

Variant links:

COSMIC-nc: COSV69456967

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0821 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+38049A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0351

AC:

5297

AN:

150882

Hom.:

123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0350

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0303

Gnomad ASJ

AF:

0.0250

Gnomad EAS

AF:

0.0890

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0219

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0340

Gnomad OTH

AF:

0.0300

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

GnomAD4 genome

AF:

0.0351

AC:

5301

AN:

151000

Hom.:

123

Cov.:

AF XY:

0.0343

AC XY:

2533

AN XY:

73758

show subpopulations

African (AFR)

AF:

0.0350

AC:

1447

AN:

41374

American (AMR)

AF:

0.0304

AC:

459

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.0250

AC:

AN:

3438

East Asian (EAS)

AF:

0.0888

AC:

456

AN:

5134

South Asian (SAS)

AF:

0.0268

AC:

129

AN:

4822

European-Finnish (FIN)

AF:

0.0219

AC:

232

AN:

10608

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0340

AC:

2287

AN:

67232

Other (OTH)

AF:

0.0297

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

265

530

794

1059

1324

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:

0.0342

Hom.:

Bravo

AF:

0.0381

Asia WGS

AF:

0.0440

AC:

153

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.015

(source)

DANN

Benign

0.46

PhyloP100

-3.0

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