Genetic Variant ENSG00000227579:n.71+33700G>T (chr1-177886382-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664407.1(ENSG00000227579):n.71+33700G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,096 control chromosomes in the GnomAD database, including 2,266 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 0.17 ( 2266 hom., cov: 32)

Consequence

ENSG00000227579
ENST00000664407.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Publications

31 publications found

Variant links:

Genes affected

ENSG00000227579 (HGNC:):

ENSG00000227579 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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
ENSG00000227579	ENST00000664407.1 link	n.71+33700G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25266

AN:

151976

Hom.:

2267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.196

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.166

AC:

25273

AN:

152096

Hom.:

2266

Cov.:

AF XY:

0.167

AC XY:

12382

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.109

AC:

4505

AN:

41506

American (AMR)

AF:

0.195

AC:

2978

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3468

East Asian (EAS)

AF:

0.171

AC:

881

AN:

5160

South Asian (SAS)

AF:

0.148

AC:

715

AN:

4816

European-Finnish (FIN)

AF:

0.182

AC:

1930

AN:

10586

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.196

AC:

13301

AN:

67976

Other (OTH)

AF:

0.161

AC:

339

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1029

2058

3087

4116

5145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

286

572

858

1144

1430

<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:

0.180

Hom.:

6671

Bravo

AF:

0.165

Asia WGS

AF:

0.138

AC:

477

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.8

(source)

DANN

Benign

0.82

PhyloP100

-0.075

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