dbSNP rs1333226: ENSG00000306409:n.191+12797A>G (chr6-137485318-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000818123.1(ENSG00000306409):n.191+12797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,324 control chromosomes in the GnomAD database, including 416 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 0.055 ( 416 hom., cov: 32)

Consequence

ENSG00000306409
ENST00000818123.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.577

Publications

3 publications found

Variant links:

Genes affected

ENSG00000306409 (HGNC:):

ENSG00000306409 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 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
ENSG00000306409	ENST00000818123.1 link	n.191+12797A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0549

AC:

8361

AN:

152204

Hom.:

414

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0326

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0592

Gnomad FIN

AF:

0.0201

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0233

Gnomad OTH

AF:

0.0554

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

GnomAD4 genome

AF:

0.0550

AC:

8378

AN:

152324

Hom.:

416

Cov.:

AF XY:

0.0549

AC XY:

4093

AN XY:

74494

show subpopulations

African (AFR)

AF:

0.133

AC:

5515

AN:

41544

American (AMR)

AF:

0.0325

AC:

497

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3472

East Asian (EAS)

AF:

0.000385

AC:

AN:

5194

South Asian (SAS)

AF:

0.0594

AC:

287

AN:

4828

European-Finnish (FIN)

AF:

0.0201

AC:

214

AN:

10624

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0233

AC:

1587

AN:

68032

Other (OTH)

AF:

0.0548

AC:

116

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

393

787

1180

1574

1967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0449

Hom.:

Bravo

AF:

0.0594

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

-0.83

CADD

Benign

3.2

(source)

DANN

Benign

0.83

PhyloP100

-0.58

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