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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904304	XR_007066375.1	n.66+106245T>C		intron_variant	Intron 2 of 3

Ensembl

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

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 v4.3

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;