rs703027

Variant names:

• chr10-28351986-T-C
• rs703027

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.203 AC: 8401 AN: 41320

American (AMR) AF: 0.262 AC: 3984 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2502 AN: 5146

South Asian (SAS) AF: 0.350 AC: 1683 AN: 4808

European-Finnish (FIN) AF: 0.235 AC: 2451 AN: 10420

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13500 AN: 67922

Other (OTH) AF: 0.219 AC: 459 AN: 2100

Alfa AF: 0.210 Hom.: 5873

Bravo AF: 0.230

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs703027; hg19: chr10-28640915;