rs999986

chr14-95337519-C-A

Variant summary

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

The XR_007064319.1(LOC124903371):n.1670G>T 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 0.243 in 152,240 control chromosomes in the GnomAD database, including 5,320 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 0.24 (5320 hom., cov: 33)
• Consequence: LOC124903371 XR_007064319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

LOC124903371 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903371	XR_007064319.1	n.1670G>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 37012 AN: 152122 Hom.: 5326 Cov.: 33

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.243 AC: 37007 AN: 152240 Hom.: 5320 Cov.: 33 AF XY: 0.244 AC XY: 18143 AN XY: 74446

Gnomad4 AFR AF: 0.0930

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.260

Alfa AF: 0.288 Hom.: 13515

Bravo AF: 0.245

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999986; hg19: chr14-95803856;