Genetic Variant ENSG00000289865:n.*88T>C (chr4-10119565-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 ENST00000701208.2(ENSG00000289865):n.*88T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,112 control chromosomes in the GnomAD database, including 8,631 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 ( 8631 hom., cov: 33)

Consequence

ENSG00000289865
ENST00000701208.2 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Publications

7 publications found

Variant links:

Genes affected

ENSG00000289865 (HGNC:58731):

ENSG00000289865 links:

LOC124900666 (HGNC:):

LOC124900666 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900666	XR_007058030.1 link	n.*88T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000289865	ENST00000701208.2 link	n.*88T>C	downstream_gene_variant
ENSG00000289865	ENST00000818624.1 link	n.*86T>C	downstream_gene_variant
ENSG00000289865	ENST00000818625.1 link	n.*88T>C	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49774

AN:

151994

Hom.:

8623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.344

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

GnomAD4 genome

AF:

0.327

AC:

49798

AN:

152112

Hom.:

8631

Cov.:

AF XY:

0.328

AC XY:

24363

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.215

AC:

8935

AN:

41500

American (AMR)

AF:

0.355

AC:

5425

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.374

AC:

1297

AN:

3472

East Asian (EAS)

AF:

0.194

AC:

1007

AN:

5180

South Asian (SAS)

AF:

0.284

AC:

1366

AN:

4812

European-Finnish (FIN)

AF:

0.395

AC:

4177

AN:

10574

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.390

AC:

26532

AN:

67978

Other (OTH)

AF:

0.342

AC:

723

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1736

3472

5207

6943

8679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.355

Hom.:

1731

Bravo

AF:

0.317

Asia WGS

AF:

0.242

AC:

845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.56

(source)

DANN

Benign

0.55

PhyloP100

-2.0

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