Genetic Variant ENSG00000263745:n.197-9961T>C (chr18-1916607-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 ENST00000584867.1(ENSG00000263745):n.197-9961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.64 ( 28810 hom., cov: 19)

Consequence

ENSG00000263745
ENST00000584867.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.484

Publications

5 publications found

Variant links:

Genes affected

ENSG00000263745 (HGNC:):

ENSG00000263745 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000263745	ENST00000584867.1	TSL:2	n.197-9961T>C	intron	N/A
ENSG00000266602	ENST00000653094.1		n.527-39980A>G	intron	N/A
ENSG00000266602	ENST00000653330.1		n.452+44676A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

88426

AN:

138134

Hom.:

28780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.698

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.722

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.671

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.594

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.663

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

GnomAD4 genome

AF:

0.640

AC:

88486

AN:

138206

Hom.:

28810

Cov.:

AF XY:

0.640

AC XY:

42575

AN XY:

66514

show subpopulations

African (AFR)

AF:

0.698

AC:

25478

AN:

36502

American (AMR)

AF:

0.723

AC:

9414

AN:

13026

Ashkenazi Jewish (ASJ)

AF:

0.624

AC:

2127

AN:

3410

East Asian (EAS)

AF:

0.671

AC:

3167

AN:

4718

South Asian (SAS)

AF:

0.669

AC:

2989

AN:

4466

European-Finnish (FIN)

AF:

0.557

AC:

4656

AN:

8354

Middle Eastern (MID)

AF:

0.566

AC:

154

AN:

272

European-Non Finnish (NFE)

AF:

0.597

AC:

38610

AN:

64700

Other (OTH)

AF:

0.667

AC:

1255

AN:

1882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

1130

2260

3389

4519

5649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.612

Hom.:

40452

Bravo

AF:

0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.9

(source)

DANN

Benign

0.59

PhyloP100

0.48

Splicing

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

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