chr18-65487125-A-T

Variant names:

• chr18-65487125-A-T
• rs4455070
• XR_935583.2:n.277+10777T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_935583.2(LOC105372169):​n.277+10777T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,880 control chromosomes in the GnomAD database, including 11,765 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 0.38 (11765 hom., cov: 32)
• Consequence: LOC105372169 XR_935583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 3 publications found

Genes affected

LOC105372169 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57738 AN: 151762 Hom.: 11761 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.380 AC: 57748 AN: 151880 Hom.: 11765 Cov.: 32 AF XY: 0.381 AC XY: 28265 AN XY: 74216

African (AFR) AF: 0.237 AC: 9805 AN: 41454

American (AMR) AF: 0.363 AC: 5532 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3063 AN: 5146

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4233 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29573 AN: 67910

Other (OTH) AF: 0.397 AC: 833 AN: 2100

Alfa AF: 0.392 Hom.: 1492

Bravo AF: 0.377

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	7.3
DANN	Benign	0.82
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs4455070; hg19: chr18-63154361;