dbSNP rs10494096: 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:

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 = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC7	NM_001144937.3 link	c.1112-28G>A		intron_variant	Intron 6 of 12	ENST00000370017.9	NP_001138409.1	Q5VTL7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC7	ENST00000370017.9 link	c.1112-28G>A		intron_variant	Intron 6 of 12	5	NM_001144937.3	ENSP00000359034.3		Q5VTL7
FNDC7	ENST00000445274.1 link	c.437-28G>A		intron_variant	Intron 2 of 7	1		ENSP00000405986.1		H7C2H6

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over