rs1741099

chr14-63315449-C-Achr14-63315449-C-Gchr14-63315449-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145171.4(GPHB5):c.204+2197G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,864 control chromosomes in the GnomAD database, including 12,196 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 0.38 (12196 hom., cov: 32)
• Consequence: GPHB5 NM_145171.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

Genes affected

GPHB5 (HGNC:18055): (glycoprotein hormone subunit beta 5) GPHB5 is a cystine knot-forming polypeptide and a subunit of the dimeric glycoprotein hormone family (Hsu et al., 2002 [PubMed 12089349]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.045).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPHB5	NM_145171.4	c.204+2197G>T		intron_variant		ENST00000621500.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPHB5	ENST00000621500.2	c.204+2197G>T		intron_variant		3	NM_145171.4	P1
GPHB5	ENST00000314140.2	c.204+2197G>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57912 AN: 151746 Hom.: 12161 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.382 AC: 57995 AN: 151864 Hom.: 12196 Cov.: 32 AF XY: 0.375 AC XY: 27851 AN XY: 74200

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.310

Alfa AF: 0.331 Hom.: 14688

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	0.045

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1741099; hg19: -;