rs17439885

Positions:

• chr18-53637140-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.53637140A>G		intergenic_region
LOC124904304	XR_007066375.1	n.66+106245T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.438

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17439885; hg19: chr18-51163510;