rs1549050

Variant names:

• chr18-29188221-C-A
• rs1549050
• XR_935327.3:n.281-6327G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-29188221-C-A
• chr18-29188221-C-T

Variant summary

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

The XR_935327.3(LOC105372044):​n.281-6327G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 152,066 control chromosomes in the GnomAD database, including 64,371 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 0.92 (64371 hom., cov: 32)
• Consequence: LOC105372044 XR_935327.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 0 publications found

Genes affected

LOC105372044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.917 AC: 139390 AN: 151948 Hom.: 64333 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.917 AC: 139480 AN: 152066 Hom.: 64371 Cov.: 32 AF XY: 0.920 AC XY: 68425 AN XY: 74338

African (AFR) AF: 0.800 AC: 33177 AN: 41482

American (AMR) AF: 0.961 AC: 14650 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3397 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5146 AN: 5152

South Asian (SAS) AF: 0.980 AC: 4729 AN: 4826

European-Finnish (FIN) AF: 0.969 AC: 10285 AN: 10610

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65029 AN: 67966

Other (OTH) AF: 0.937 AC: 1981 AN: 2114

Alfa AF: 0.943 Hom.: 48793

Bravo AF: 0.911

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.27
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1549050; hg19: chr18-26768186;