rs1479067

Variant names:

• chr5-101814850-C-A
• rs1479067
• XR_007058891.1:n.294+807G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-101814850-C-A
• chr5-101814850-C-G
• chr5-101814850-C-T

Variant summary

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

The XR_948628.3(LOC105379102):​n.294+807G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 151,866 control chromosomes in the GnomAD database, including 40,902 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 0.73 (40902 hom., cov: 31)
• Consequence: LOC105379102 XR_948628.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 4 publications found

Genes affected

LOC105379102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.732 AC: 111034 AN: 151748 Hom.: 40858 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.732 AC: 111132 AN: 151866 Hom.: 40902 Cov.: 31 AF XY: 0.737 AC XY: 54718 AN XY: 74206

African (AFR) AF: 0.660 AC: 27347 AN: 41410

American (AMR) AF: 0.794 AC: 12111 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4179 AN: 5178

South Asian (SAS) AF: 0.773 AC: 3723 AN: 4814

European-Finnish (FIN) AF: 0.773 AC: 8178 AN: 10582

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.750 AC: 50867 AN: 67844

Other (OTH) AF: 0.719 AC: 1514 AN: 2106

Alfa AF: 0.742 Hom.: 30458

Bravo AF: 0.731

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.33
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs1479067; hg19: chr5-101150554; COSMIC: COSV60723889;