rs488846

Variant names:

• chr18-54261400-T-C
• rs488846
• XR_007066379.1:n.81-239A>G

Variant summary

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

The XR_007066379.1(LOC124904307):​n.81-239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,894 control chromosomes in the GnomAD database, including 5,092 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 0.25 (5092 hom., cov: 31)
• Consequence: LOC124904307 XR_007066379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

Genes affected

LOC124904307 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904307	XR_007066379.1	n.81-239A>G		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38512 AN: 151776 Hom.: 5093 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.254 AC: 38519 AN: 151894 Hom.: 5092 Cov.: 31 AF XY: 0.249 AC XY: 18505 AN XY: 74240

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.0295

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.259

Alfa AF: 0.278 Hom.: 735

Bravo AF: 0.251

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488846; hg19: chr18-51787770;