Genetic Variant ENSG00000301182:n.209-17710T>C (chr4-89858672-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000776860.1(ENSG00000301182):n.209-17710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,020 control chromosomes in the GnomAD database, including 41,762 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 0.74 ( 41762 hom., cov: 31)

Consequence

ENSG00000301182
ENST00000776860.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Publications

10 publications found

Variant links:

Genes affected

ENSG00000301182 (HGNC:):

ENSG00000301182 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301182	ENST00000776860.1 link	n.209-17710T>C	intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1 link	n.183-17710T>C	intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1 link	n.81-3626T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.738

AC:

112170

AN:

151900

Hom.:

41745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.818

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.646

Gnomad EAS

AF:

0.859

Gnomad SAS

AF:

0.615

Gnomad FIN

AF:

0.813

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.721

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

GnomAD4 genome

AF:

0.738

AC:

112222

AN:

152020

Hom.:

41762

Cov.:

AF XY:

0.735

AC XY:

54631

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.704

AC:

29178

AN:

41442

American (AMR)

AF:

0.660

AC:

10060

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.646

AC:

2241

AN:

3468

East Asian (EAS)

AF:

0.859

AC:

4438

AN:

5166

South Asian (SAS)

AF:

0.615

AC:

2955

AN:

4808

European-Finnish (FIN)

AF:

0.813

AC:

8610

AN:

10586

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.769

AC:

52286

AN:

67976

Other (OTH)

AF:

0.716

AC:

1515

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1489

2977

4466

5954

7443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<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:

0.756

Hom.:

67524

Bravo

AF:

0.732

Asia WGS

AF:

0.711

AC:

2469

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.8

(source)

DANN

Benign

0.41

PhyloP100

-0.12

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