dbSNP rs7678651: ENSG00000301182:n.209-6258G>T (chr4-89847220-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000776860.1(ENSG00000301182):n.209-6258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,952 control chromosomes in the GnomAD database, including 8,048 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 0.31 ( 8048 hom., cov: 32)

Consequence

ENSG00000301182
ENST00000776860.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.927

Publications

7 publications found

Variant links:

Genes affected

ENSG00000301182 (HGNC:):

ENSG00000301182 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301182	ENST00000776860.1 link	n.209-6258G>T	intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1 link	n.183-6258G>T	intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1 link	n.204-6258G>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46467

AN:

151834

Hom.:

8053

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.284

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

GnomAD4 genome

AF:

0.306

AC:

46455

AN:

151952

Hom.:

8048

Cov.:

AF XY:

0.304

AC XY:

22561

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.154

AC:

6381

AN:

41442

American (AMR)

AF:

0.265

AC:

4046

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1123

AN:

3468

East Asian (EAS)

AF:

0.300

AC:

1550

AN:

5162

South Asian (SAS)

AF:

0.225

AC:

1085

AN:

4822

European-Finnish (FIN)

AF:

0.428

AC:

4501

AN:

10526

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.394

AC:

26741

AN:

67956

Other (OTH)

AF:

0.280

AC:

590

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1611

3221

4832

6442

8053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.360

Hom.:

2885

Bravo

AF:

0.287

Asia WGS

AF:

0.232

AC:

809

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.59

(source)

DANN

Benign

0.78

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