dbSNP rs1867504: INHCAP:n.268A>G (chr3-133691817-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000475455.1(INHCAP):n.268A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,316 control chromosomes in the GnomAD database, including 27,859 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 0.60 ( 27749 hom., cov: 33)

Exomes 𝑓: 0.49 ( 110 hom. )

Consequence

INHCAP
ENST00000475455.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Publications

17 publications found

Variant links:

Genes affected

INHCAP (HGNC:11759): (inhibitor of carbonic anhydrase pseudogene)

INHCAP links:

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 Gene-Disease associations (from GenCC):

atransferrinemia
Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, Genomics England PanelApp

TF links:

ENSG00000291042 (HGNC:):

ENSG00000291042 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=-0.74).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TF	NM_001354703.2 link	c.-940+3453A>G		intron_variant	Intron 2 of 22		NP_001341632.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
INHCAP	ENST00000475455.1 link	n.268A>G	non_coding_transcript_exon_variant	Exon 2 of 10	6
ENSG00000291042	ENST00000460564.5 link	n.209+3453A>G	intron_variant	Intron 2 of 4	4
ENSG00000291042	ENST00000490470.5 link	n.209+3453A>G	intron_variant	Intron 2 of 3	4
ENSG00000291042	ENST00000497521.5 link	n.208+3453A>G	intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90361

AN:

151332

Hom.:

27705

Cov.:

show subpopulations

Gnomad AFR

AF:

0.743

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.521

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.579

GnomAD4 exome

AF:

0.488

AC:

422

AN:

864

Hom.:

110

Cov.:

AF XY:

0.478

AC XY:

255

AN XY:

534

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.528

AC:

299

AN:

566

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.424

AC:

AN:

224

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.597

AC:

90464

AN:

151452

Hom.:

27749

Cov.:

AF XY:

0.598

AC XY:

44265

AN XY:

74000

show subpopulations

African (AFR)

AF:

0.743

AC:

30672

AN:

41272

American (AMR)

AF:

0.572

AC:

8713

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

1737

AN:

3458

East Asian (EAS)

AF:

0.522

AC:

2675

AN:

5120

South Asian (SAS)

AF:

0.471

AC:

2264

AN:

4808

European-Finnish (FIN)

AF:

0.614

AC:

6433

AN:

10482

Middle Eastern (MID)

AF:

0.555

AC:

162

AN:

292

European-Non Finnish (NFE)

AF:

0.533

AC:

36102

AN:

67770

Other (OTH)

AF:

0.578

AC:

1213

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1842

3684

5526

7368

9210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.552

Hom.:

55047

Bravo

AF:

0.605

Asia WGS

AF:

0.548

AC:

1906

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

6.3

(source)

DANN

Benign

0.81

PhyloP100

2.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over