rs703027

chr10-28351986-T-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 0.224 in 151,616 control chromosomes in the GnomAD database, including 4,068 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 0.22 (4068 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 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: 0.223 AC: 33855 AN: 151500 Hom.: 4055 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.224 AC: 33905 AN: 151616 Hom.: 4068 Cov.: 31 AF XY: 0.229 AC XY: 16947 AN XY: 74022

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.219

Alfa AF: 0.209 Hom.: 4635

Bravo AF: 0.230

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.9
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703027; hg19: chr10-28640915;