XR_001744259.1:n.1244-77242C>T

Variant names:

• chr6-90830814-C-T
• rs1504281
• XR_001744259.1:n.1244-77242C>T

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-77242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,938 control chromosomes in the GnomAD database, including 21,056 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 0.52 (21056 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 2 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78907 AN: 151820 Hom.: 21029 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.520 AC: 78984 AN: 151938 Hom.: 21056 Cov.: 32 AF XY: 0.530 AC XY: 39381 AN XY: 74254

African (AFR) AF: 0.597 AC: 24695 AN: 41398

American (AMR) AF: 0.616 AC: 9409 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3527 AN: 5156

South Asian (SAS) AF: 0.557 AC: 2676 AN: 4808

European-Finnish (FIN) AF: 0.540 AC: 5712 AN: 10570

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29650 AN: 67952

Other (OTH) AF: 0.529 AC: 1114 AN: 2106

Alfa AF: 0.467 Hom.: 14960

Bravo AF: 0.527

Asia WGS AF: 0.666 AC: 2315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1504281; hg19: chr6-91540532;