rs11001702

Variant names:

• chr10-52343665-T-C
• rs11001702

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 0.174 in 152,058 control chromosomes in the GnomAD database, including 3,184 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 0.17 (3184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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: 0.174 AC: 26425 AN: 151940 Hom.: 3175 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.174 AC: 26465 AN: 152058 Hom.: 3184 Cov.: 32 AF XY: 0.175 AC XY: 13010 AN XY: 74346

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0782

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0913

Gnomad4 OTH AF: 0.160

Alfa AF: 0.107 Hom.: 2287

Bravo AF: 0.190

Asia WGS AF: 0.309 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11001702; hg19: chr10-54103425;