chr14-67234451-C-A

Position:

• chr14-67234451-C-A

Variant summary

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

The XR_007064217.1(LOC124903330):​n.2121-3324G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,042 control chromosomes in the GnomAD database, including 20,449 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 0.47 (20449 hom., cov: 31)
• Consequence: LOC124903330 XR_007064217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

LOC124903330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903330	XR_007064217.1	n.2121-3324G>T		intron_variant, non_coding_transcript_variant
GPHN	XM_047430879.1	c.1312+175665C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71873 AN: 151924 Hom.: 20460 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.473 AC: 71851 AN: 152042 Hom.: 20449 Cov.: 31 AF XY: 0.476 AC XY: 35332 AN XY: 74298

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.497

Alfa AF: 0.601 Hom.: 49126

Bravo AF: 0.445

Asia WGS AF: 0.473 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1290900; hg19: chr14-67701168;