dbSNP rs4252053: ENSG00000224477:n.1038A>G (chr6-160701242-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000448126.6(ENSG00000224477):n.1038A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,194 control chromosomes in the GnomAD database, including 1,349 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 0.13 ( 1349 hom., cov: 32)

Consequence

ENSG00000224477
ENST00000448126.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.70

Publications

5 publications found

Variant links:

Genes affected

ENSG00000224477 (HGNC:):

ENSG00000224477 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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
ENSG00000224477	ENST00000448126.6 link	n.1038A>G		non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19538

AN:

152076

Hom.:

1346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0882

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.00481

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.129

AC:

19558

AN:

152194

Hom.:

1349

Cov.:

AF XY:

0.126

AC XY:

9391

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0882

AC:

3667

AN:

41560

American (AMR)

AF:

0.123

AC:

1881

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

572

AN:

3470

East Asian (EAS)

AF:

0.00482

AC:

AN:

5182

South Asian (SAS)

AF:

0.128

AC:

616

AN:

4818

European-Finnish (FIN)

AF:

0.117

AC:

1242

AN:

10596

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11076

AN:

67972

Other (OTH)

AF:

0.119

AC:

250

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

787

1575

2362

3150

3937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<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:

0.139

Hom.:

201

Bravo

AF:

0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.057

(source)

DANN

Benign

0.63

PhyloP100

-3.7

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