Genetic Variant ENSG00000287709:n.212-6262G>C (chr5-57658989-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 ENST00000661344.3(ENSG00000287709):n.212-6262G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,896 control chromosomes in the GnomAD database, including 11,779 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 0.34 ( 11779 hom., cov: 32)

Consequence

ENSG00000287709
ENST00000661344.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

0 publications found

Variant links:

Genes affected

ENSG00000287709 (HGNC:):

ENSG00000287709 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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928505	NR_104668.1 link	n.101-6262G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287709	ENST00000661344.3 link	n.212-6262G>C	intron_variant	Intron 1 of 2
ENSG00000287709	ENST00000685494.1 link	n.105-6262G>C	intron_variant	Intron 1 of 2
ENSG00000287709	ENST00000688166.1 link	n.89-6262G>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52160

AN:

151778

Hom.:

11736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.335

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

GnomAD4 genome

AF:

0.344

AC:

52270

AN:

151896

Hom.:

11779

Cov.:

AF XY:

0.340

AC XY:

25283

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.645

AC:

26718

AN:

41402

American (AMR)

AF:

0.269

AC:

4109

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

728

AN:

3464

East Asian (EAS)

AF:

0.311

AC:

1606

AN:

5158

South Asian (SAS)

AF:

0.153

AC:

736

AN:

4804

European-Finnish (FIN)

AF:

0.258

AC:

2728

AN:

10586

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.217

AC:

14737

AN:

67920

Other (OTH)

AF:

0.334

AC:

705

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1503

3007

4510

6014

7517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.276

Hom.:

894

Bravo

AF:

0.361

Asia WGS

AF:

0.297

AC:

1032

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.6

(source)

DANN

Benign

0.84

PhyloP100

-1.1

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