rs8015529

Variant names:

• chr14-98035882-C-G
• rs8015529
• XR_001750874.2:n.2973G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC107984706 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.317 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

African (AFR) AF: 0.260 AC: 10807 AN: 41510

American (AMR) AF: 0.403 AC: 6156 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3466

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4808

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10548

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22825 AN: 67978

Other (OTH) AF: 0.326 AC: 688 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.048
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs8015529; hg19: chr14-98502219;