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_007058891.1(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_007058891.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379102	XR_007058891.1	n.294+807G>T		intron_variant	Intron 2 of 5
LOC105379102	XR_948628.3	n.294+807G>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;