Variant 2-219572359-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000243786.3(INHA):c.-16C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,613,276 control chromosomes in the GnomAD database, including 32,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.18 ( 2677 hom., cov: 33)

Exomes 𝑓: 0.20 ( 30127 hom. )

Consequence

INHA
ENST00000243786.3 5_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.694

Variant links:

Genes affected

INHA (HGNC:6065): (inhibin subunit alpha) This gene encodes a member of the TGF-beta (transforming growth factor-beta) superfamily of proteins. The encoded preproprotein is proteolytically processed to generate multiple peptide products, including the alpha subunit of the inhibin A and B protein complexes. These complexes negatively regulate follicle stimulating hormone secretion from the pituitary gland. Inhibins have also been implicated in regulating numerous cellular processes including cell proliferation, apoptosis, immune response and hormone secretion. Mutations in this gene may be associated with male infertility and premature ovarian failure in female human patients. [provided by RefSeq, Aug 2016]

INHA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INHA	NM_002191.4 linkuse as main transcript	c.-16C>T		5_prime_UTR_variant	1/2	ENST00000243786.3	NP_002182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHA	ENST00000243786.3 linkuse as main transcript	c.-16C>T		5_prime_UTR_variant	1/2	1	NM_002191.4	ENSP00000243786	P1
INHA	ENST00000489456.1 linkuse as main transcript	n.286-2335C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27837

AN:

152050

Hom.:

2680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.0911

Gnomad FIN

AF:

0.196

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.190

AC:

47742

AN:

251360

Hom.:

4864

AF XY:

0.185

AC XY:

25136

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.171

Gnomad EAS exome

AF:

0.197

Gnomad SAS exome

AF:

0.0924

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.200

AC:

291695

AN:

1461108

Hom.:

30127

Cov.:

AF XY:

0.196

AC XY:

142304

AN XY:

726856

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.253

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.169

Gnomad4 SAS exome

AF:

0.0943

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.183

AC:

27842

AN:

152168

Hom.:

2677

Cov.:

AF XY:

0.182

AC XY:

13553

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.240

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.0924

Gnomad4 FIN

AF:

0.196

Gnomad4 NFE

AF:

0.204

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.191

Hom.:

762

Bravo

AF:

0.187

Asia WGS

AF:

0.127

AC:

441

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Jun 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

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