rs8015529

Positions:

• chr14-98035882-C-G
• chr14-98035882-C-T

Variant summary

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

The XR_001750874.2(LOC107984706):​n.2973G>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 0.317 in 152,074 control chromosomes in the GnomAD database, including 7,961 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 0.32 (7961 hom., cov: 33)
• Consequence: LOC107984706 XR_001750874.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

LOC107984706 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984706	XR_001750874.2	n.2973G>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48230 AN: 151956 Hom.: 7951 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.317 AC: 48252 AN: 152074 Hom.: 7961 Cov.: 33 AF XY: 0.317 AC XY: 23561 AN XY: 74324

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.326

Alfa AF: 0.310 Hom.: 910

Bravo AF: 0.326

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.048
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8015529; hg19: chr14-98502219;