rs10503051

Variant names:

• chr18-61226757-C-T
• rs10503051

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 0.00878 in 152,084 control chromosomes in the GnomAD database, including 19 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 0.0088 (19 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0588 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: 0.00883 AC: 1342 AN: 151966 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.00347

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.00368

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00686

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.00878 AC: 1336 AN: 152084 Hom.: 19 Cov.: 32 AF XY: 0.00935 AC XY: 695 AN XY: 74336

Gnomad4 AFR AF: 0.00229

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.00347

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.00368

Gnomad4 NFE AF: 0.00686

Gnomad4 OTH AF: 0.00758

Alfa AF: 0.00731 Hom.: 2

Bravo AF: 0.0109

Asia WGS AF: 0.0530 AC: 184 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.028
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503051; hg19: chr18-58893990;