rs3759757

chr14-67611110-G-C

Variant summary

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

The ENST00000559594.1(ENSG00000259502):n.125G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 154,256 control chromosomes in the GnomAD database, including 18,079 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 0.43 (17956 hom., cov: 31)
  • Exomes 𝑓: 0.31 (123 hom.)
• Consequence: ENST00000559594.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPHN	XM_047430879.1	c.1313-124085G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559594.1	n.125G>C		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65181 AN: 151834 Hom.: 17900 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.306 AC: 704 AN: 2304 Hom.: 123 Cov.: 0 AF XY: 0.305 AC XY: 340 AN XY: 1114

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.348

Gnomad4 FIN exome AF: 0.256

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.576

GnomAD4 genome AF: 0.430 AC: 65307 AN: 151952 Hom.: 17956 Cov.: 31 AF XY: 0.427 AC XY: 31680 AN XY: 74254

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.441

Alfa AF: 0.362 Hom.: 1624

Bravo AF: 0.457

Asia WGS AF: 0.428 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759757; hg19: chr14-68077827;