14-83972417-C-T

Variant names:

• chr14-83972417-C-T
• rs2210185
• XM_047432045.1:c.100-934G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064377.1(LOC124903401):​n.170+2317G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,768 control chromosomes in the GnomAD database, including 20,648 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 0.52 (20648 hom., cov: 32)
• Consequence: LOC124903401 XR_007064377.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 0 publications found

Genes affected

LOC124903401 (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 (SAS) allele frequency at 95% confidence interval = 0.557 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: 0.515 AC: 78165 AN: 151650 Hom.: 20618 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.516 AC: 78255 AN: 151768 Hom.: 20648 Cov.: 32 AF XY: 0.510 AC XY: 37878 AN XY: 74218

African (AFR) AF: 0.541 AC: 22315 AN: 41248

American (AMR) AF: 0.536 AC: 8165 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1833 AN: 5162

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4820

European-Finnish (FIN) AF: 0.410 AC: 4322 AN: 10550

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35469 AN: 67962

Other (OTH) AF: 0.550 AC: 1159 AN: 2106

Alfa AF: 0.517 Hom.: 7411

Bravo AF: 0.529

Asia WGS AF: 0.492 AC: 1709 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	0.51
DANN	Benign	0.55
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2210185; hg19: chr14-84438761;