rs999986

Variant names:

• chr14-95337519-C-A
• rs999986
• XR_007064319.1:n.1670G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC124903371 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0930 AC: 3862 AN: 41540

American (AMR) AF: 0.321 AC: 4910 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2495 AN: 5178

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2604 AN: 10602

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19774 AN: 68010

Other (OTH) AF: 0.260 AC: 549 AN: 2110

Alfa AF: 0.282 Hom.: 27427

Bravo AF: 0.245

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs999986; hg19: chr14-95803856;