Genetic Variant ENSG00000284823:n.721+72A>G (chr6-4677726-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 ENST00000716074.1(ENSG00000284823):n.721+72A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,014 control chromosomes in the GnomAD database, including 4,321 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 0.22 ( 4321 hom., cov: 33)

Consequence

ENSG00000284823
ENST00000716074.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

4 publications found

Variant links:

Genes affected

ENSG00000284823 (HGNC:):

ENSG00000284823 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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
ENSG00000284823	ENST00000716074.1 link	n.721+72A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32802

AN:

151896

Hom.:

4321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0746

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.179

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.200

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

GnomAD4 genome

AF:

0.216

AC:

32811

AN:

152014

Hom.:

4321

Cov.:

AF XY:

0.221

AC XY:

16444

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.0748

AC:

3100

AN:

41470

American (AMR)

AF:

0.220

AC:

3353

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

690

AN:

3472

East Asian (EAS)

AF:

0.322

AC:

1663

AN:

5158

South Asian (SAS)

AF:

0.356

AC:

1714

AN:

4818

European-Finnish (FIN)

AF:

0.310

AC:

3272

AN:

10554

Middle Eastern (MID)

AF:

0.166

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.267

AC:

18125

AN:

67964

Other (OTH)

AF:

0.202

AC:

426

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1257

2513

3770

5026

6283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.228

Hom.:

761

Bravo

AF:

0.200

Asia WGS

AF:

0.320

AC:

1112

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.9

(source)

DANN

Benign

0.63

PhyloP100

0.12

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