dbSNP rs10795668: ENSG00000297769:n.102-40C>T (chr10-8659256-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000750870.1(ENSG00000297769):n.102-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,092 control chromosomes in the GnomAD database, including 5,644 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 ( 5644 hom., cov: 32)

Consequence

ENSG00000297769
ENST00000750870.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

165 publications found

Variant links:

Genes affected

ENSG00000297769 (HGNC:):

ENSG00000297769 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000750870.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750870.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000297769	ENST00000750870.1	n.102-40C>T	intron	N/A
ENSG00000297769	ENST00000750865.1	n.-38C>T	upstream_gene	N/A
ENSG00000297769	ENST00000750866.1	n.-40C>T	upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37314

AN:

151976

Hom.:

5627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0607

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.273

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

GnomAD4 genome

AF:

0.246

AC:

37340

AN:

152092

Hom.:

5644

Cov.:

AF XY:

0.247

AC XY:

18331

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0605

AC:

2513

AN:

41526

American (AMR)

AF:

0.311

AC:

4750

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

1059

AN:

3470

East Asian (EAS)

AF:

0.369

AC:

1901

AN:

5158

South Asian (SAS)

AF:

0.248

AC:

1193

AN:

4818

European-Finnish (FIN)

AF:

0.292

AC:

3083

AN:

10562

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.321

AC:

21848

AN:

67982

Other (OTH)

AF:

0.277

AC:

586

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1358

2716

4073

5431

6789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.301

Hom.:

33530

Bravo

AF:

0.239

Asia WGS

AF:

0.299

AC:

1040

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.33

PhyloP100

0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over