dbSNP rs8177252: TF:c.1203+2001C>A (chr3-133761330-C-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_001063.4(TF):c.1203+2001C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 158,634 control chromosomes in the GnomAD database, including 8,333 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 0.32 ( 7901 hom., cov: 31)

Exomes 𝑓: 0.35 ( 432 hom. )

Consequence

TF
NM_001063.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.19

Publications

3 publications found

Variant links:

Genes affected

TF (HGNC:11740): (transferrin) This gene encodes a glycoprotein with an approximate molecular weight of 76.5 kDa. It is thought to have been created as a result of an ancient gene duplication event that led to generation of homologous C and N-terminal domains each of which binds one ion of ferric iron. The function of this protein is to transport iron from the intestine, reticuloendothelial system, and liver parenchymal cells to all proliferating cells in the body. This protein may also have a physiologic role as granulocyte/pollen-binding protein (GPBP) involved in the removal of certain organic matter and allergens from serum. [provided by RefSeq, Sep 2009]

TF links:

ACSL3P1 (HGNC:56529): (ACSL3 pseudogene 1)

ACSL3P1 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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TF	NM_001063.4 link	c.1203+2001C>A	intron_variant	Intron 9 of 16	ENST00000402696.9	NP_001054.2	P02787Q06AH7A0PJA6
TF	NM_001354703.2 link	c.1071+2001C>A	intron_variant	Intron 15 of 22		NP_001341632.2
TF	NM_001354704.2 link	c.822+2001C>A	intron_variant	Intron 8 of 15		NP_001341633.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TF	ENST00000402696.9 link	c.1203+2001C>A		intron_variant	Intron 9 of 16	1	NM_001063.4	ENSP00000385834.3		P02787
ACSL3P1	ENST00000474389.1 link	n.1031C>A		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47914

AN:

151654

Hom.:

7889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.318

GnomAD4 exome

AF:

0.345

AC:

2370

AN:

6862

Hom.:

432

Cov.:

AF XY:

0.340

AC XY:

1452

AN XY:

4274

show subpopulations

African (AFR)

AF:

0.209

AC:

AN:

172

American (AMR)

AF:

0.509

AC:

357

AN:

702

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

AN:

144

East Asian (EAS)

AF:

0.414

AC:

163

AN:

394

South Asian (SAS)

AF:

0.425

AC:

291

AN:

684

European-Finnish (FIN)

AF:

0.308

AC:

267

AN:

866

Middle Eastern (MID)

AF:

0.286

AC:

AN:

European-Non Finnish (NFE)

AF:

0.311

AC:

1109

AN:

3568

Other (OTH)

AF:

0.333

AC:

106

AN:

318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

156

233

311

389

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.316

AC:

47968

AN:

151772

Hom.:

7901

Cov.:

AF XY:

0.318

AC XY:

23545

AN XY:

74140

show subpopulations

African (AFR)

AF:

0.242

AC:

10031

AN:

41424

American (AMR)

AF:

0.387

AC:

5895

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

988

AN:

3464

East Asian (EAS)

AF:

0.425

AC:

2190

AN:

5150

South Asian (SAS)

AF:

0.424

AC:

2032

AN:

4796

European-Finnish (FIN)

AF:

0.286

AC:

3001

AN:

10508

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.336

AC:

22804

AN:

67884

Other (OTH)

AF:

0.320

AC:

673

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1629

3258

4886

6515

8144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.240

Hom.:

1116

Bravo

AF:

0.320

Asia WGS

AF:

0.402

AC:

1399

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.2

(source)

DANN

Benign

0.56

PhyloP100

2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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