rs17102387

chr10-121657064-G-C

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 0.154 in 151,998 control chromosomes in the GnomAD database, including 2,256 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 0.15 (2256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914

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 (AFR) allele frequency at 95% confidence interval = 0.262 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: 0.154 AC: 23341 AN: 151878 Hom.: 2260 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.154 AC: 23349 AN: 151998 Hom.: 2256 Cov.: 32 AF XY: 0.157 AC XY: 11693 AN XY: 74288

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.128

Alfa AF: 0.118 Hom.: 175

Bravo AF: 0.164

Asia WGS AF: 0.159 AC: 556 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	4.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17102387; hg19: chr10-123416578;