Genetic Variant ENST00000498289.5:n.851+32372C>G (chr1-169716304-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000498289.5(FIRRM):n.851+32372C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,134 control chromosomes in the GnomAD database, including 1,521 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 0.14 ( 1521 hom., cov: 32)

Consequence

FIRRM
ENST00000498289.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.743

Publications

4 publications found

Variant links:

Genes affected

FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

FIRRM 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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
FIRRM	ENST00000498289.5 link	n.851+32372C>G		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

20986

AN:

152016

Hom.:

1522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0612

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.145

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

GnomAD4 genome

AF:

0.138

AC:

20999

AN:

152134

Hom.:

1521

Cov.:

AF XY:

0.139

AC XY:

10334

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.122

AC:

5058

AN:

41502

American (AMR)

AF:

0.175

AC:

2671

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

574

AN:

3472

East Asian (EAS)

AF:

0.0616

AC:

318

AN:

5164

South Asian (SAS)

AF:

0.191

AC:

922

AN:

4820

European-Finnish (FIN)

AF:

0.127

AC:

1347

AN:

10600

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9614

AN:

67994

Other (OTH)

AF:

0.143

AC:

302

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

945

1890

2834

3779

4724

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.0650

Hom.:

Bravo

AF:

0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.58

(source)

DANN

Benign

0.72

PhyloP100

-0.74

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