chr14-67416907-A-C

Position:

• chr14-67416907-A-C

Variant summary

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

The XM_047430879.1(GPHN):​c.1313-318288A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,204 control chromosomes in the GnomAD database, including 11,522 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 0.31 (11522 hom., cov: 33)
• Consequence: GPHN XM_047430879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83

Genes affected

GPHN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPHN	XM_047430879.1	c.1313-318288A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46745 AN: 152086 Hom.: 11489 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.308 AC: 46840 AN: 152204 Hom.: 11522 Cov.: 33 AF XY: 0.313 AC XY: 23292 AN XY: 74426

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.302

Alfa AF: 0.153 Hom.: 2843

Bravo AF: 0.341

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.044
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17248895; hg19: chr14-67883624;