rs10503083

Variant names:

• chr18-63576250-A-T
• rs10503083

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.147 AC: 6082 AN: 41504

American (AMR) AF: 0.0289 AC: 442 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3468

East Asian (EAS) AF: 0.0312 AC: 161 AN: 5166

South Asian (SAS) AF: 0.0546 AC: 263 AN: 4818

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1259 AN: 68002

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10503083; hg19: chr18-61243483;