rs10863399

chr1-218453334-A-C

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 0.225 in 152,170 control chromosomes in the GnomAD database, including 4,244 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 0.23 (4244 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

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 = 0.307 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: 0.225 AC: 34258 AN: 152052 Hom.: 4239 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.225 AC: 34280 AN: 152170 Hom.: 4244 Cov.: 33 AF XY: 0.223 AC XY: 16577 AN XY: 74408

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.222

Alfa AF: 0.222 Hom.: 727

Bravo AF: 0.228

Asia WGS AF: 0.149 AC: 517 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	6.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10863399; hg19: chr1-218626676;