rs2803546

Positions:

• chr10-86647298-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;