Genetic Variant ENSG00000223716:n.155-111T>C (chr9-38375218-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 ENST00000422554.2(ENSG00000223716):n.155-111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,188 control chromosomes in the GnomAD database, including 40,182 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 0.71 ( 40176 hom., cov: 32)

Exomes 𝑓: 1.0 ( 6 hom. )

Consequence

ENSG00000223716
ENST00000422554.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.472

Publications

3 publications found

Variant links:

Genes affected

ENSG00000223716 (HGNC:):

ENSG00000223716 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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107987065	XR_001746668.2 link	n.369-76T>C	intron_variant	Intron 2 of 3
LOC107987065	XR_001746669.2 link	n.269-76T>C	intron_variant	Intron 3 of 4
LOC107987065	XR_001746670.2 link	n.368+2241T>C	intron_variant	Intron 2 of 2
LOC105376040	XR_929605.1 link	n.321+55A>G	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223716	ENST00000422554.2 link	n.155-111T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108716

AN:

152056

Hom.:

40145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.807

Gnomad ASJ

AF:

0.814

Gnomad EAS

AF:

0.790

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.841

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.746

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.715

AC:

108799

AN:

152176

Hom.:

40176

Cov.:

AF XY:

0.719

AC XY:

53527

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.508

AC:

21080

AN:

41494

American (AMR)

AF:

0.807

AC:

12345

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.814

AC:

2821

AN:

3466

East Asian (EAS)

AF:

0.789

AC:

4085

AN:

5176

South Asian (SAS)

AF:

0.787

AC:

3795

AN:

4824

European-Finnish (FIN)

AF:

0.841

AC:

8917

AN:

10608

Middle Eastern (MID)

AF:

0.779

AC:

229

AN:

294

European-Non Finnish (NFE)

AF:

0.781

AC:

53105

AN:

67998

Other (OTH)

AF:

0.747

AC:

1575

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1486

2971

4457

5942

7428

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.766

Hom.:

29164

Bravo

AF:

0.704

Asia WGS

AF:

0.780

AC:

2712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.4

(source)

DANN

Benign

0.56

PhyloP100

0.47

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over