rs17101921

chr10-121393781-G-A

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 0.0391 in 152,204 control chromosomes in the GnomAD database, including 299 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 0.039 (299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

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 = 0.149 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: 0.0391 AC: 5939 AN: 152086 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.00650

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0391 AC: 5957 AN: 152204 Hom.: 299 Cov.: 32 AF XY: 0.0429 AC XY: 3193 AN XY: 74416

Gnomad4 AFR AF: 0.00648

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0373

Alfa AF: 0.0297 Hom.: 238

Bravo AF: 0.0427

Asia WGS AF: 0.0750 AC: 259 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	5.2
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17101921; hg19: chr10-123153295;