Genetic Variant ENST00000818771.1:n.639+2089T>C (chr7-95437694-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 ENST00000818771.1(ENSG00000233942):n.639+2089T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,966 control chromosomes in the GnomAD database, including 9,092 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 0.33 ( 9092 hom., cov: 31)

Consequence

ENSG00000233942
ENST00000818771.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.880

Publications

13 publications found

Variant links:

Genes affected

ENSG00000233942 (HGNC:):

ENSG00000233942 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000233942	ENST00000818771.1 link	n.639+2089T>C	intron_variant	Intron 2 of 8
ENSG00000233942	ENST00000818772.1 link	n.464-32998T>C	intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1 link	n.553+2089T>C	intron_variant	Intron 2 of 5
ENSG00000233942	ENST00000818774.1 link	n.118+2089T>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50475

AN:

151850

Hom.:

9089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.339

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

GnomAD4 genome

AF:

0.332

AC:

50488

AN:

151966

Hom.:

9092

Cov.:

AF XY:

0.325

AC XY:

24146

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.239

AC:

9914

AN:

41458

American (AMR)

AF:

0.245

AC:

3743

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1316

AN:

3466

East Asian (EAS)

AF:

0.140

AC:

726

AN:

5170

South Asian (SAS)

AF:

0.297

AC:

1430

AN:

4814

European-Finnish (FIN)

AF:

0.364

AC:

3833

AN:

10520

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.417

AC:

28359

AN:

67950

Other (OTH)

AF:

0.336

AC:

707

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1638

3275

4913

6550

8188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.380

Hom.:

19289

Bravo

AF:

0.316

Asia WGS

AF:

0.208

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.88

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