Variant 16-72076424-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_020995.4(HPR):c.390G>T(p.Gly130Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,591,186 control chromosomes in the GnomAD database, including 323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 20 hom., cov: 32)

Exomes 𝑓: 0.011 ( 303 hom. )

Consequence

HPR
NM_020995.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0840

Variant links:

Genes affected

HPR (HGNC:5156): (haptoglobin-related protein) This gene encodes a haptoglobin-related protein that binds hemoglobin as efficiently as haptoglobin. Unlike haptoglobin, plasma concentration of this protein is unaffected in patients with sickle cell anemia and extensive intravascular hemolysis, suggesting a difference in binding between haptoglobin-hemoglobin and haptoglobin-related protein-hemoglobin complexes to CD163, the hemoglobin scavenger receptor. This protein may also be a clinically important predictor of recurrence of breast cancer. [provided by RefSeq, Oct 2011]

HPR links:

TXNL4B (HGNC:):

TXNL4B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-72076424-G-T is Benign according to our data. Variant chr16-72076424-G-T is described in ClinVar as [Benign]. Clinvar id is 791062.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0136 (2065/152172) while in subpopulation NFE AF= 0.0232 (1575/68018). AF 95% confidence interval is 0.0222. There are 20 homozygotes in gnomad4. There are 943 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HPR	NM_020995.4 linkuse as main transcript	c.390G>T	p.Gly130Gly	synonymous_variant	5/5	ENST00000540303.7	NP_066275.3	P00739-1
HPR	NM_001384360.1 linkuse as main transcript	c.30G>T	p.Gly10Gly	synonymous_variant	6/6		NP_001371289.1
HPR	XM_024450251.2 linkuse as main transcript	c.408G>T	p.Gly136Gly	synonymous_variant	5/5		XP_024306019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPR	ENST00000540303.7 linkuse as main transcript	c.390G>T	p.Gly130Gly	synonymous_variant	5/5	1	NM_020995.4	ENSP00000441828.2		P00739-1
TXNL4B	ENST00000562153.5 linkuse as main transcript	c.284+12563C>A		intron_variant		4		ENSP00000454635.2		H3BN11

Frequencies

GnomAD3 genomes

AF:

0.0136

AC:

2064

AN:

152054

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00401

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00453

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0232

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.00662

AC:

1633

AN:

246758

Hom.:

AF XY:

0.00631

AC XY:

844

AN XY:

133786

show subpopulations

Gnomad AFR exome

AF:

0.00233

Gnomad AMR exome

AF:

0.00605

Gnomad ASJ exome

AF:

0.00411

Gnomad EAS exome

AF:

0.000223

Gnomad SAS exome

AF:

0.00102

Gnomad FIN exome

AF:

0.00275

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.00832

GnomAD4 exome

AF:

0.0105

AC:

15149

AN:

1439014

Hom.:

303

Cov.:

AF XY:

0.0102

AC XY:

7306

AN XY:

716388

show subpopulations

Gnomad4 AFR exome

AF:

0.00243

Gnomad4 AMR exome

AF:

0.00707

Gnomad4 ASJ exome

AF:

0.00607

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.00118

Gnomad4 FIN exome

AF:

0.00507

Gnomad4 NFE exome

AF:

0.0125

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.0136

AC:

2065

AN:

152172

Hom.:

Cov.:

AF XY:

0.0127

AC XY:

943

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.00400

Gnomad4 AMR

AF:

0.0112

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.000582

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00453

Gnomad4 NFE

AF:

0.0232

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.0139

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.42

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.42

Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over