dbSNP rs17216887: ENSG00000246090:n.266C>G (chr4-99089122-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000500358.6(ENSG00000246090):n.266C>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 0.0324 in 189,386 control chromosomes in the GnomAD database, including 167 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 0.032 ( 129 hom., cov: 32)

Exomes 𝑓: 0.034 ( 38 hom. )

Consequence

ENSG00000246090
ENST00000500358.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

6 publications found

Variant links:

Genes affected

ENSG00000246090 (HGNC:):

ENSG00000246090 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=-0.8).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.032 (4880/152304) while in subpopulation NFE AF = 0.0508 (3458/68024). AF 95% confidence interval is 0.0494. There are 129 homozygotes in GnomAd4. There are 2355 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 129 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1 link	n.266C>G		non_coding_transcript_exon_variant	Exon 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000246090	ENST00000500358.6 link	n.266C>G	non_coding_transcript_exon_variant	Exon 1 of 10	1
ENSG00000246090	ENST00000499178.3 link	n.253C>G	non_coding_transcript_exon_variant	Exon 1 of 3	3
ENSG00000246090	ENST00000661393.1 link	n.263C>G	non_coding_transcript_exon_variant	Exon 1 of 10

Frequencies

GnomAD3 genomes

AF:

0.0321

AC:

4880

AN:

152186

Hom.:

129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00900

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0147

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.0537

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0508

Gnomad OTH

AF:

0.0277

GnomAD4 exome

AF:

0.0339

AC:

1258

AN:

37082

Hom.:

Cov.:

AF XY:

0.0328

AC XY:

636

AN XY:

19394

show subpopulations

African (AFR)

AF:

0.00435

AC:

AN:

1150

American (AMR)

AF:

0.0101

AC:

AN:

1282

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

AN:

1220

East Asian (EAS)

AF:

0.00

AC:

AN:

1884

South Asian (SAS)

AF:

0.0164

AC:

AN:

4260

European-Finnish (FIN)

AF:

0.0482

AC:

117

AN:

2428

Middle Eastern (MID)

AF:

0.0119

AC:

AN:

168

European-Non Finnish (NFE)

AF:

0.0425

AC:

953

AN:

22402

Other (OTH)

AF:

0.0345

AC:

AN:

2288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

110

164

219

274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0320

AC:

4880

AN:

152304

Hom.:

129

Cov.:

AF XY:

0.0316

AC XY:

2355

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.00897

AC:

373

AN:

41568

American (AMR)

AF:

0.0146

AC:

224

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5176

South Asian (SAS)

AF:

0.0155

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0537

AC:

570

AN:

10616

Middle Eastern (MID)

AF:

0.0205

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0508

AC:

3458

AN:

68024

Other (OTH)

AF:

0.0274

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

242

483

725

966

1208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0477

Hom.:

Bravo

AF:

0.0281

Asia WGS

AF:

0.00635

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.4

(source)

DANN

Benign

0.47

PhyloP100

-1.6

PromoterAI

0.046

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over