rs11006027

Variant names:

• chr10-58045035-C-T
• rs11006027

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 0.193 in 152,058 control chromosomes in the GnomAD database, including 3,017 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 0.19 (3017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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 = 0.248 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: 0.193 AC: 29286 AN: 151938 Hom.: 3007 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.193 AC: 29314 AN: 152058 Hom.: 3017 Cov.: 32 AF XY: 0.193 AC XY: 14335 AN XY: 74344

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.186

Alfa AF: 0.181 Hom.: 607

Bravo AF: 0.189

Asia WGS AF: 0.182 AC: 632 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	0.25
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11006027; hg19: chr10-59804795;