dbSNP rs10485083: ENSG00000226281:n.329+16792G>C (chr6-6784051-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 ENST00000689004.1(ENSG00000226281):n.329+16792G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 152,228 control chromosomes in the GnomAD database, including 793 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 0.066 ( 793 hom., cov: 32)

Consequence

ENSG00000226281
ENST00000689004.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396

Publications

1 publications found

Variant links:

Genes affected

ENSG00000226281 (HGNC:):

ENSG00000226281 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928004	NR_187687.1 link	n.485+10099G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000226281	ENST00000689004.1 link	n.329+16792G>C	intron_variant	Intron 1 of 4
ENSG00000226281	ENST00000702519.1 link	n.504+10099G>C	intron_variant	Intron 2 of 2
ENSG00000226281	ENST00000775982.1 link	n.264+10099G>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0657

AC:

9997

AN:

152110

Hom.:

787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0683

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.0495

Gnomad FIN

AF:

0.00707

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00531

Gnomad OTH

AF:

0.0516

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

GnomAD4 genome

AF:

0.0659

AC:

10035

AN:

152228

Hom.:

793

Cov.:

AF XY:

0.0659

AC XY:

4903

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.176

AC:

7319

AN:

41506

American (AMR)

AF:

0.0685

AC:

1048

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3468

East Asian (EAS)

AF:

0.157

AC:

812

AN:

5182

South Asian (SAS)

AF:

0.0499

AC:

241

AN:

4826

European-Finnish (FIN)

AF:

0.00707

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00529

AC:

360

AN:

68022

Other (OTH)

AF:

0.0510

AC:

108

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

423

846

1269

1692

2115

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0401

Hom.:

Bravo

AF:

0.0757

Asia WGS

AF:

0.104

AC:

361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.9

(source)

DANN

Benign

0.46

PhyloP100

-0.40

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