rs2803546

Variant names:

• chr10-86647298-G-A
• rs2803546

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 0.401 in 152,002 control chromosomes in the GnomAD database, including 12,745 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 0.40 (12745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 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: 0.401 AC: 60939 AN: 151882 Hom.: 12740 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.401 AC: 60974 AN: 152002 Hom.: 12745 Cov.: 32 AF XY: 0.401 AC XY: 29757 AN XY: 74278

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.370

Alfa AF: 0.433 Hom.: 7558

Bravo AF: 0.380

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2803546; hg19: chr10-88407055;