XR_001753538.1:n.511+15978C>A

Variant names:

• chr18-52127533-C-A
• rs4401133
• XR_001753538.1:n.511+15978C>A

Variant summary

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

The XR_001753538.1(LOC105372121):​n.511+15978C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,178 control chromosomes in the GnomAD database, including 2,234 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 0.15 (2234 hom., cov: 32)
• Consequence: LOC105372121 XR_001753538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 1 publications found

Genes affected

LOC105372121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.155 AC: 23530 AN: 152060 Hom.: 2225 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.155 AC: 23540 AN: 152178 Hom.: 2234 Cov.: 32 AF XY: 0.156 AC XY: 11588 AN XY: 74384

African (AFR) AF: 0.0411 AC: 1706 AN: 41546

American (AMR) AF: 0.151 AC: 2303 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1515 AN: 5168

South Asian (SAS) AF: 0.194 AC: 937 AN: 4828

European-Finnish (FIN) AF: 0.242 AC: 2557 AN: 10576

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13529 AN: 67990

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.186 Hom.: 1490

Bravo AF: 0.143

Asia WGS AF: 0.270 AC: 935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.26
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4401133; hg19: chr18-49653903;