rs10518783

Variant names:

• chr15-54828982-C-G
• rs10518783

Your query was ambiguous. Multiple possible variants found:

• chr15-54828982-C-G
• chr15-54828982-C-T

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 0.264 in 151,930 control chromosomes in the GnomAD database, including 5,704 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 0.26 (5704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.264 AC: 40099 AN: 151812 Hom.: 5690 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.264 AC: 40149 AN: 151930 Hom.: 5704 Cov.: 32 AF XY: 0.258 AC XY: 19167 AN XY: 74238

African (AFR) AF: 0.355 AC: 14712 AN: 41394

American (AMR) AF: 0.229 AC: 3494 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3472

East Asian (EAS) AF: 0.0453 AC: 234 AN: 5166

South Asian (SAS) AF: 0.195 AC: 936 AN: 4804

European-Finnish (FIN) AF: 0.203 AC: 2140 AN: 10560

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17022 AN: 67942

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.254 Hom.: 646

Bravo AF: 0.267

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.3
DANN	Benign	0.72
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs10518783; hg19: chr15-55121180;