rs7144243

Positions:

• chr14-67607715-A-G

Variant summary

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

The XM_047430879.1(GPHN):​c.1313-127480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,090 control chromosomes in the GnomAD database, including 3,327 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 0.21 (3327 hom., cov: 32)
• Consequence: GPHN XM_047430879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

GPHN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPHN	XM_047430879.1	c.1313-127480A>G		intron_variant			XP_047286835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31303 AN: 151972 Hom.: 3324 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0595

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.206 AC: 31326 AN: 152090 Hom.: 3327 Cov.: 32 AF XY: 0.207 AC XY: 15387 AN XY: 74350

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.232

Alfa AF: 0.214 Hom.: 4518

Bravo AF: 0.199

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7144243; hg19: chr14-68074432;