chr10-28351986-T-C

Variant names:

• chr10-28351986-T-C
• rs703027

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;