Genetic Variant ENSG00000224746:n.607+19710C>T (chr7-135794825-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000419211.3(ENSG00000224746):n.607+19710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,172 control chromosomes in the GnomAD database, including 3,845 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 0.21 ( 3845 hom., cov: 33)

Consequence

ENSG00000224746
ENST00000419211.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

4 publications found

Variant links:

Genes affected

ENSG00000224746 (HGNC:):

ENSG00000224746 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000224746	ENST00000419211.3 link	n.607+19710C>T	intron_variant	Intron 1 of 2	2
ENSG00000224746	ENST00000830862.1 link	n.609+19710C>T	intron_variant	Intron 1 of 2
ENSG00000224746	ENST00000830863.1 link	n.615+19710C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31411

AN:

152052

Hom.:

3814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.279

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.207

AC:

31497

AN:

152172

Hom.:

3845

Cov.:

AF XY:

0.203

AC XY:

15138

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.329

AC:

13638

AN:

41486

American (AMR)

AF:

0.280

AC:

4275

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

413

AN:

3470

East Asian (EAS)

AF:

0.188

AC:

971

AN:

5178

South Asian (SAS)

AF:

0.129

AC:

624

AN:

4824

European-Finnish (FIN)

AF:

0.100

AC:

1060

AN:

10604

Middle Eastern (MID)

AF:

0.161

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.146

AC:

9926

AN:

68002

Other (OTH)

AF:

0.209

AC:

442

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1248

2496

3743

4991

6239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.168

Hom.:

6736

Bravo

AF:

0.226

Asia WGS

AF:

0.196

AC:

681

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.65

PhyloP100

-0.37

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