XR_007064276.1:n.196A>G

Variant names:

• chr14-77260014-A-G
• rs369202
• XR_007064276.1:n.196A>G

Variant summary

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

The XR_007064276.1(LOC124903351):​n.196A>G 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 0.823 in 152,114 control chromosomes in the GnomAD database, including 51,667 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 0.82 (51667 hom., cov: 31)
• Consequence: LOC124903351 XR_007064276.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 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: 0.823 AC: 125074 AN: 151996 Hom.: 51617 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.823 AC: 125180 AN: 152114 Hom.: 51667 Cov.: 31 AF XY: 0.825 AC XY: 61358 AN XY: 74364

African (AFR) AF: 0.856 AC: 35512 AN: 41488

American (AMR) AF: 0.765 AC: 11689 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2966 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4935 AN: 5170

South Asian (SAS) AF: 0.809 AC: 3897 AN: 4816

European-Finnish (FIN) AF: 0.847 AC: 8973 AN: 10600

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54448 AN: 67978

Other (OTH) AF: 0.836 AC: 1767 AN: 2114

Alfa AF: 0.824 Hom.: 6427

Bravo AF: 0.820

Asia WGS AF: 0.888 AC: 3091 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	4.2
DANN	Benign	0.35
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs369202; hg19: chr14-77726357;