dbSNP rs73100934: INHBA:c.-199A>G (chr7-41703060-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002192.4(INHBA):c.-199A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,338 control chromosomes in the GnomAD database, including 328 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 0.055 ( 327 hom., cov: 32)

Exomes 𝑓: 0.22 ( 1 hom. )

Consequence

INHBA
NM_002192.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531

Publications

4 publications found

Variant links:

Genes affected

INHBA (HGNC:6066): (inhibin subunit beta A) This gene encodes a member of the TGF-beta (transforming growth factor-beta) superfamily of proteins. The encoded preproprotein is proteolytically processed to generate a subunit of the dimeric activin and inhibin protein complexes. These complexes activate and inhibit, respectively, follicle stimulating hormone secretion from the pituitary gland. The encoded protein also plays a role in eye, tooth and testis development. Elevated expression of this gene may be associated with cancer cachexia in human patients. [provided by RefSeq, Aug 2016]

INHBA links:

INHBA-AS1 (HGNC:40303): (INHBA antisense RNA 1)

INHBA-AS1 links:

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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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INHBA	NM_002192.4 link	c.-199A>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000242208.5	NP_002183.1	P08476A4D1W7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBA	ENST00000242208.5 link	c.-199A>G		5_prime_UTR_variant	Exon 1 of 3	1	NM_002192.4	ENSP00000242208.4		P08476

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8424

AN:

152202

Hom.:

328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.0681

Gnomad ASJ

AF:

0.0603

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0250

Gnomad FIN

AF:

0.0549

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0825

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.222

AC:

AN:

Hom.:

Cov.:

AF XY:

0.286

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0553

AC:

8424

AN:

152320

Hom.:

327

Cov.:

AF XY:

0.0539

AC XY:

4015

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.0155

AC:

646

AN:

41570

American (AMR)

AF:

0.0682

AC:

1043

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0603

AC:

209

AN:

3468

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0251

AC:

121

AN:

4828

European-Finnish (FIN)

AF:

0.0549

AC:

583

AN:

10618

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0825

AC:

5615

AN:

68026

Other (OTH)

AF:

0.0605

AC:

128

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

407

815

1222

1630

2037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0684

Hom.:

153

Bravo

AF:

0.0555

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

0.53

PromoterAI

-0.0081

Neutral

(source)

Mutation Taster

=300/0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over