Genetic Variant ENST00000662211.1:n.548+65740G>A (chr5-104170027-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000662211.1(NIHCOLE):n.548+65740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,108 control chromosomes in the GnomAD database, including 403 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 0.064 ( 403 hom., cov: 32)

Consequence

NIHCOLE
ENST00000662211.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.557

Publications

2 publications found

Variant links:

COSMIC-nc: COSV60176499

Genes affected

NIHCOLE (HGNC:53024): (ncRNA involved in NHEJ oncogenic ligation efficiency)

NIHCOLE 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
NIHCOLE	ENST00000662211.1 link	n.548+65740G>A	intron_variant	Intron 4 of 5
NIHCOLE	ENST00000666145.1 link	n.522+65740G>A	intron_variant	Intron 4 of 4
NIHCOLE	ENST00000721479.1 link	n.522+65740G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0642

AC:

9758

AN:

151990

Hom.:

405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0182

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.0815

Gnomad ASJ

AF:

0.0689

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.0812

Gnomad FIN

AF:

0.0672

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0788

Gnomad OTH

AF:

0.0583

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

GnomAD4 genome

AF:

0.0641

AC:

9757

AN:

152108

Hom.:

403

Cov.:

AF XY:

0.0650

AC XY:

4832

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0182

AC:

756

AN:

41540

American (AMR)

AF:

0.0814

AC:

1243

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.0689

AC:

239

AN:

3468

East Asian (EAS)

AF:

0.165

AC:

853

AN:

5158

South Asian (SAS)

AF:

0.0812

AC:

392

AN:

4826

European-Finnish (FIN)

AF:

0.0672

AC:

711

AN:

10576

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0788

AC:

5357

AN:

67956

Other (OTH)

AF:

0.0568

AC:

120

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

465

931

1396

1862

2327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

122

244

366

488

610

<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:

0.0775

Hom.:

398

Bravo

AF:

0.0640

Asia WGS

AF:

0.111

AC:

387

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.7

(source)

DANN

Benign

0.45

PhyloP100

0.56

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