rs10483556

Variant names:

• chr14-49493524-A-G
• rs10483556

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 0.188 in 152,216 control chromosomes in the GnomAD database, including 2,906 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 0.19 (2906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.188 AC: 28599 AN: 152098 Hom.: 2901 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28624 AN: 152216 Hom.: 2906 Cov.: 32 AF XY: 0.188 AC XY: 13994 AN XY: 74418

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.188

Alfa AF: 0.170 Hom.: 387

Bravo AF: 0.187

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483556; hg19: chr14-49960242;