dbSNP rs200978: ENSG00000305770:n.1710C>G (chr6-27885390-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 ENST00000812862.1(ENSG00000305770):n.1710C>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 0.266 in 152,018 control chromosomes in the GnomAD database, including 6,331 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 0.27 ( 6331 hom., cov: 32)

Consequence

ENSG00000305770
ENST00000812862.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.927

Publications

7 publications found

Variant links:

Genes affected

ENSG00000305770 (HGNC:):

ENSG00000305770 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 = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000305770	ENST00000812862.1 link	n.1710C>G	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000305770	ENST00000812856.1 link	n.364-2209C>G	intron_variant	Intron 1 of 1
ENSG00000305770	ENST00000812857.1 link	n.476-2209C>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40374

AN:

151900

Hom.:

6301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.266

AC:

40457

AN:

152018

Hom.:

6331

Cov.:

AF XY:

0.261

AC XY:

19397

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.432

AC:

17889

AN:

41438

American (AMR)

AF:

0.236

AC:

3608

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

500

AN:

3470

East Asian (EAS)

AF:

0.144

AC:

744

AN:

5174

South Asian (SAS)

AF:

0.221

AC:

1065

AN:

4822

European-Finnish (FIN)

AF:

0.157

AC:

1661

AN:

10554

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.208

AC:

14105

AN:

67974

Other (OTH)

AF:

0.243

AC:

514

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1402

2804

4206

5608

7010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.237

Hom.:

599

Bravo

AF:

0.278

Asia WGS

AF:

0.214

AC:

744

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

0.63

(source)

DANN

Benign

0.38

PhyloP100

-0.93

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