dbSNP rs16851585: ENSG00000227579:n.92-22714G>C (chr1-177599664-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000438575.7(ENSG00000227579):n.92-22714G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,124 control chromosomes in the GnomAD database, including 1,663 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 0.14 ( 1663 hom., cov: 33)

Consequence

ENSG00000227579
ENST00000438575.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.467

Publications

3 publications found

Variant links:

Genes affected

ENSG00000227579 (HGNC:):

ENSG00000227579 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=-0.61).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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
ENSG00000227579	ENST00000438575.7 link	n.92-22714G>C	intron_variant	Intron 1 of 3	3
ENSG00000227579	ENST00000663166.1 link	n.277-22714G>C	intron_variant	Intron 1 of 4
ENSG00000227579	ENST00000663978.1 link	n.180-22714G>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20571

AN:

152004

Hom.:

1667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.135

AC:

20574

AN:

152124

Hom.:

1663

Cov.:

AF XY:

0.141

AC XY:

10491

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.150

AC:

6216

AN:

41486

American (AMR)

AF:

0.127

AC:

1940

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

389

AN:

3466

East Asian (EAS)

AF:

0.409

AC:

2111

AN:

5158

South Asian (SAS)

AF:

0.238

AC:

1148

AN:

4820

European-Finnish (FIN)

AF:

0.131

AC:

1380

AN:

10558

Middle Eastern (MID)

AF:

0.151

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.102

AC:

6958

AN:

68024

Other (OTH)

AF:

0.130

AC:

276

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

877

1754

2631

3508

4385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.126

Hom.:

163

Bravo

AF:

0.134

Asia WGS

AF:

0.315

AC:

1095

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

6.8

(source)

DANN

Benign

0.73

PhyloP100

0.47

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