Genetic Variant FNDC7:c.1112-28G>A (chr1-108727780-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 NM_001144937.3(FNDC7):c.1112-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,610,268 control chromosomes in the GnomAD database, including 172,673 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 0.40 ( 13176 hom., cov: 30)

Exomes 𝑓: 0.46 ( 159497 hom. )

Consequence

FNDC7
NM_001144937.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Publications

5 publications found

Variant links:

Genes affected

FNDC7 (HGNC:26668): (fibronectin type III domain containing 7) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

FNDC7 links:

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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 = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144937.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC7	NM_001144937.3	MANE Select	c.1112-28G>A		intron	N/A	NP_001138409.1	Q5VTL7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FNDC7	ENST00000370017.9	TSL:5 MANE Select	c.1112-28G>A	intron	N/A	ENSP00000359034.3	Q5VTL7
FNDC7	ENST00000445274.1	TSL:1	c.437-28G>A	intron	N/A	ENSP00000405986.1	H7C2H6
FNDC7	ENST00000932418.1		c.1112-852G>A	intron	N/A	ENSP00000602477.1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61020

AN:

151724

Hom.:

13169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.487

Gnomad OTH

AF:

0.385

GnomAD2 exomes

AF:

0.428

AC:

106271

AN:

248426

AF XY:

0.437

show subpopulations

Gnomad AFR exome

AF:

0.267

Gnomad AMR exome

AF:

0.357

Gnomad ASJ exome

AF:

0.444

Gnomad EAS exome

AF:

0.188

Gnomad FIN exome

AF:

0.504

Gnomad NFE exome

AF:

0.486

Gnomad OTH exome

AF:

0.441

GnomAD4 exome

AF:

0.463

AC:

675394

AN:

1458428

Hom.:

159497

Cov.:

AF XY:

0.464

AC XY:

336676

AN XY:

725348

show subpopulations

African (AFR)

AF:

0.260

AC:

8699

AN:

33448

American (AMR)

AF:

0.355

AC:

15835

AN:

44652

Ashkenazi Jewish (ASJ)

AF:

0.445

AC:

11505

AN:

25826

East Asian (EAS)

AF:

0.192

AC:

7633

AN:

39690

South Asian (SAS)

AF:

0.460

AC:

39430

AN:

85798

European-Finnish (FIN)

AF:

0.505

AC:

26851

AN:

53176

Middle Eastern (MID)

AF:

0.436

AC:

2456

AN:

5636

European-Non Finnish (NFE)

AF:

0.483

AC:

536500

AN:

1109938

Other (OTH)

AF:

0.439

AC:

26485

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

17315

34631

51946

69262

86577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15570

31140

46710

62280

77850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.402

AC:

61041

AN:

151840

Hom.:

13176

Cov.:

AF XY:

0.402

AC XY:

29821

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.276

AC:

11426

AN:

41408

American (AMR)

AF:

0.329

AC:

5022

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1581

AN:

3470

East Asian (EAS)

AF:

0.192

AC:

986

AN:

5146

South Asian (SAS)

AF:

0.457

AC:

2197

AN:

4808

European-Finnish (FIN)

AF:

0.508

AC:

5356

AN:

10536

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.487

AC:

33062

AN:

67918

Other (OTH)

AF:

0.381

AC:

801

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1726

3453

5179

6906

8632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<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:

0.455

Hom.:

63443

Bravo

AF:

0.383

Asia WGS

AF:

0.307

AC:

1073

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.7

(source)

DANN

Benign

0.51

PhyloP100

-0.065

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over