rs10503083

Positions:

• chr18-63576250-A-T

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 0.0573 in 152,142 control chromosomes in the GnomAD database, including 488 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 0.057 (488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8703 AN: 152024 Hom.: 489 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0573 AC: 8716 AN: 152142 Hom.: 488 Cov.: 33 AF XY: 0.0569 AC XY: 4234 AN XY: 74392

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.0312

Gnomad4 SAS AF: 0.0546

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0429 Hom.: 42

Bravo AF: 0.0607

Asia WGS AF: 0.0690 AC: 239 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503083; hg19: chr18-61243483;