XR_007064276.1:n.817G>C

Variant names:

• chr14-77260635-G-C
• rs747273
• XR_007064276.1:n.817G>C

Variant summary

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

The XR_007064276.1(LOC124903351):​n.817G>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 0.34 in 152,212 control chromosomes in the GnomAD database, including 10,559 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 0.34 (10559 hom., cov: 34)
• Consequence: LOC124903351 XR_007064276.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 2 publications found

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51680 AN: 152094 Hom.: 10558 Cov.: 34

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.340 AC: 51684 AN: 152212 Hom.: 10559 Cov.: 34 AF XY: 0.342 AC XY: 25448 AN XY: 74394

African (AFR) AF: 0.121 AC: 5040 AN: 41568

American (AMR) AF: 0.284 AC: 4343 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5154

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4828

European-Finnish (FIN) AF: 0.524 AC: 5545 AN: 10586

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30825 AN: 67984

Other (OTH) AF: 0.347 AC: 730 AN: 2106

Alfa AF: 0.413 Hom.: 1805

Bravo AF: 0.311

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs747273; hg19: chr14-77726978;