rs10483556

Variant names:

• chr14-49493524-A-G
• rs10483556

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 0.188 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.238 AC: 9879 AN: 41528

American (AMR) AF: 0.161 AC: 2460 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3472

East Asian (EAS) AF: 0.148 AC: 768 AN: 5186

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1712 AN: 10598

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11541 AN: 67998

Other (OTH) AF: 0.188 AC: 398 AN: 2112

Alfa AF: 0.172 Hom.: 405

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
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs10483556; hg19: chr14-49960242;