Genetic Variant ENST00000806122.1:n.72+20761T>G (chr6-104383628-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000806122.1(ENSG00000304752):n.72+20761T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,350 control chromosomes in the GnomAD database, including 5,030 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 0.25 ( 5030 hom., cov: 30)

Consequence

ENSG00000304752
ENST00000806122.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Publications

5 publications found

Variant links:

Genes affected

ENSG00000304752 (HGNC:):

ENSG00000304752 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304752	ENST00000806122.1 link	n.72+20761T>G		intron_variant	Intron 1 of 2
ENSG00000304752	ENST00000806123.1 link	n.158+20761T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37169

AN:

151238

Hom.:

5033

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.211

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

GnomAD4 genome

AF:

0.246

AC:

37175

AN:

151350

Hom.:

5030

Cov.:

AF XY:

0.251

AC XY:

18556

AN XY:

73932

show subpopulations

African (AFR)

AF:

0.134

AC:

5530

AN:

41402

American (AMR)

AF:

0.233

AC:

3530

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

1000

AN:

3466

East Asian (EAS)

AF:

0.333

AC:

1708

AN:

5130

South Asian (SAS)

AF:

0.348

AC:

1664

AN:

4784

European-Finnish (FIN)

AF:

0.383

AC:

3969

AN:

10362

Middle Eastern (MID)

AF:

0.212

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.282

AC:

19103

AN:

67758

Other (OTH)

AF:

0.209

AC:

438

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1354

2707

4061

5414

6768

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.266

Hom.:

18266

Bravo

AF:

0.225

Asia WGS

AF:

0.306

AC:

1065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.62

(source)

DANN

Benign

0.69

PhyloP100

-2.4

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