dbSNP rs12210810: ENSG00000301363:n.618-30708C>G (chr6-118332041-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000778490.1(ENSG00000301363):n.618-30708C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,308 control chromosomes in the GnomAD database, including 147 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 0.036 ( 147 hom., cov: 33)

Consequence

ENSG00000301363
ENST00000778490.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.25

Publications

34 publications found

Variant links:

Genes affected

ENSG00000301363 (HGNC:):

ENSG00000301363 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301363	ENST00000778490.1 link	n.618-30708C>G	intron_variant	Intron 1 of 1
ENSG00000301363	ENST00000778491.1 link	n.159-6854C>G	intron_variant	Intron 1 of 3
ENSG00000301363	ENST00000778492.1 link	n.622-7858C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0358

AC:

5446

AN:

152190

Hom.:

148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00955

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0723

Gnomad FIN

AF:

0.0356

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0534

Gnomad OTH

AF:

0.0406

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

GnomAD4 genome

AF:

0.0357

AC:

5442

AN:

152308

Hom.:

147

Cov.:

AF XY:

0.0354

AC XY:

2636

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00952

AC:

396

AN:

41576

American (AMR)

AF:

0.0270

AC:

413

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0516

AC:

179

AN:

3466

East Asian (EAS)

AF:

0.000578

AC:

AN:

5186

South Asian (SAS)

AF:

0.0718

AC:

346

AN:

4822

European-Finnish (FIN)

AF:

0.0356

AC:

378

AN:

10610

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0534

AC:

3632

AN:

68026

Other (OTH)

AF:

0.0402

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

275

549

824

1098

1373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0448

Hom.:

108

Bravo

AF:

0.0326

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.14

(source)

DANN

Benign

0.73

PhyloP100

-2.3

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