Genetic Variant ENST00000764643.1:n.49-7223C>T (chr7-37626246-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000764643.1(ENSG00000299559):n.49-7223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,420 control chromosomes in the GnomAD database, including 36,843 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 0.70 ( 36843 hom., cov: 32)

Consequence

ENSG00000299559
ENST00000764643.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.108

Publications

7 publications found

Variant links:

Genes affected

ENSG00000299559 (HGNC:):

ENSG00000299559 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 (SAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299559	ENST00000764643.1 link	n.49-7223C>T	intron_variant	Intron 1 of 2
ENSG00000299559	ENST00000764644.1 link	n.43-7223C>T	intron_variant	Intron 1 of 2
ENSG00000299559	ENST00000764645.1 link	n.149-3907C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105365

AN:

151302

Hom.:

36818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.709

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.717

Gnomad SAS

AF:

0.733

Gnomad FIN

AF:

0.719

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.712

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

GnomAD4 genome

AF:

0.696

AC:

105436

AN:

151420

Hom.:

36843

Cov.:

AF XY:

0.700

AC XY:

51827

AN XY:

74014

show subpopulations

African (AFR)

AF:

0.730

AC:

30225

AN:

41384

American (AMR)

AF:

0.710

AC:

10803

AN:

15216

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

2394

AN:

3456

East Asian (EAS)

AF:

0.716

AC:

3706

AN:

5176

South Asian (SAS)

AF:

0.733

AC:

3537

AN:

4824

European-Finnish (FIN)

AF:

0.719

AC:

7581

AN:

10546

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

44903

AN:

67510

Other (OTH)

AF:

0.708

AC:

1490

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1625

3250

4876

6501

8126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.658

Hom.:

8219

Bravo

AF:

0.702

Asia WGS

AF:

0.707

AC:

2440

AN:

3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.4

(source)

DANN

Benign

0.55

PhyloP100

0.11

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