XR_001744259.1:n.1244-77528A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-77528A>G		intron_variant	Intron 2 of 3

Ensembl

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

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 v4.3

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;