Genetic Variant ENSG00000290061:n.795T>C (chr11-65493175-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000702719.2(ENSG00000290061):n.795T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,048 control chromosomes in the GnomAD database, including 16,478 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 0.42 ( 16478 hom., cov: 31)

Consequence

ENSG00000290061
ENST00000702719.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390

Publications

30 publications found

Variant links:

Genes affected

ENSG00000290061 (HGNC:):

ENSG00000290061 links:

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new If you want to explore the variant's impact on the transcript ENST00000702719.2, 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702719.2. 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290061	ENST00000702719.2		n.795T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000300048	ENST00000768429.1		n.54A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64457

AN:

151930

Hom.:

16445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.696

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.274

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.385

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

GnomAD4 genome

AF:

0.424

AC:

64544

AN:

152048

Hom.:

16478

Cov.:

AF XY:

0.418

AC XY:

31068

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.696

AC:

28837

AN:

41426

American (AMR)

AF:

0.484

AC:

7385

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.274

AC:

951

AN:

3472

East Asian (EAS)

AF:

0.424

AC:

2194

AN:

5176

South Asian (SAS)

AF:

0.379

AC:

1826

AN:

4822

European-Finnish (FIN)

AF:

0.180

AC:

1907

AN:

10600

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20194

AN:

67976

Other (OTH)

AF:

0.380

AC:

802

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1645

3290

4935

6580

8225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<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:

0.348

Hom.:

34024

Bravo

AF:

0.466

Asia WGS

AF:

0.405

AC:

1410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.5

(source)

DANN

Benign

0.48

PhyloP100

-0.039

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

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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