rs1504279

Variant names:

• chr6-90830528-A-G
• rs1504279
• XR_001744259.1:n.1244-77528A>G

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-77528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,898 control chromosomes in the GnomAD database, including 8,414 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 0.33 (8414 hom., cov: 31)
• Consequence: LOC107986623 XR_001744259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 1 publications found

Genes affected

LOC107986623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.329 AC: 49915 AN: 151780 Hom.: 8408 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.329 AC: 49937 AN: 151898 Hom.: 8414 Cov.: 31 AF XY: 0.329 AC XY: 24449 AN XY: 74224

African (AFR) AF: 0.400 AC: 16551 AN: 41412

American (AMR) AF: 0.250 AC: 3812 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1159 AN: 5154

South Asian (SAS) AF: 0.361 AC: 1737 AN: 4812

European-Finnish (FIN) AF: 0.334 AC: 3529 AN: 10562

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21338 AN: 67934

Other (OTH) AF: 0.315 AC: 663 AN: 2102

Alfa AF: 0.318 Hom.: 3651

Bravo AF: 0.322

Asia WGS AF: 0.341 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.30
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1504279; hg19: chr6-91540246;