rs17439885

Variant names:

• chr18-53637140-A-G
• rs17439885
• XR_007066375.1:n.66+106245T>C

Variant summary

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

The XR_007066375.1(LOC124904304):​n.66+106245T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,058 control chromosomes in the GnomAD database, including 13,806 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 0.39 (13806 hom., cov: 32)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 1 publications found

Genes affected

LOC124904304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.392 AC: 59601 AN: 151940 Hom.: 13807 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.392 AC: 59603 AN: 152058 Hom.: 13806 Cov.: 32 AF XY: 0.397 AC XY: 29517 AN XY: 74330

African (AFR) AF: 0.135 AC: 5593 AN: 41516

American (AMR) AF: 0.397 AC: 6064 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2042 AN: 5174

South Asian (SAS) AF: 0.574 AC: 2771 AN: 4828

European-Finnish (FIN) AF: 0.539 AC: 5687 AN: 10550

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33930 AN: 67944

Other (OTH) AF: 0.438 AC: 926 AN: 2114

Alfa AF: 0.454 Hom.: 3376

Bravo AF: 0.364

Asia WGS AF: 0.464 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.1
DANN	Benign	0.66
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs17439885; hg19: chr18-51163510;