rs1741099

Variant names:

• chr14-63315449-C-A
• rs1741099
• NM_145171.4:c.204+2197G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-63315449-C-A
• chr14-63315449-C-G
• chr14-63315449-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145171.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPHB5	NM_145171.4	MANE Select	c.204+2197G>T		intron	N/A	NP_660154.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPHB5	ENST00000621500.2	TSL:3 MANE Select	c.204+2197G>T		intron	N/A	ENSP00000478993.1	Q86YW7
	GPHB5	ENST00000314140.2	TSL:1	c.204+2197G>T		intron	N/A	ENSP00000479431.1	Q86YW7

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

African (AFR) AF: 0.564 AC: 23355 AN: 41406

American (AMR) AF: 0.250 AC: 3819 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 966 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1756 AN: 5174

South Asian (SAS) AF: 0.137 AC: 662 AN: 4818

European-Finnish (FIN) AF: 0.340 AC: 3569 AN: 10490

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22971 AN: 67934

Other (OTH) AF: 0.310 AC: 653 AN: 2106

Alfa AF: 0.344 Hom.: 36547

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.045
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs1741099;