2-120351868-G-A

Variant names:

• chr2-120351868-G-A
• rs57802235
• NM_002193.4:c.*1994G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002193.4(INHBB):​c.*1994G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,220 control chromosomes in the GnomAD database, including 1,811 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 0.12 (1811 hom., cov: 33)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: INHBB NM_002193.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 4 publications found

Genes affected

INHBB (HGNC:6067): (inhibin subunit beta B) 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. Polymorphisms near this gene are associated with pre-eclampsia in female human patients. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002193.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBB	NM_002193.4	MANE Select	c.*1994G>A		downstream_gene	N/A	NP_002184.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBB	ENST00000295228.4	TSL:1 MANE Select	c.*1994G>A		downstream_gene	N/A	ENSP00000295228.3

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18174 AN: 152074 Hom.: 1806 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0852

GnomAD4 exome AF: 0.0714 AC: 2 AN: 28 Hom.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.120 AC: 18202 AN: 152192 Hom.: 1811 Cov.: 33 AF XY: 0.123 AC XY: 9177 AN XY: 74424

African (AFR) AF: 0.203 AC: 8427 AN: 41492

American (AMR) AF: 0.173 AC: 2646 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2306 AN: 5168

South Asian (SAS) AF: 0.0632 AC: 305 AN: 4826

European-Finnish (FIN) AF: 0.0788 AC: 836 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0486 AC: 3306 AN: 68018

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0760 Hom.: 245

Bravo AF: 0.136

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs57802235; hg19: chr2-121109444;