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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372044	XR_935327.3	n.281-6327G>T		intron_variant	Intron 3 of 4

Ensembl

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

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 v4.3

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;