rs10483556

chr14-49493524-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;