rs17102387

Variant names:

• chr10-121657064-G-C
• rs17102387

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 0.154 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.266 AC: 11029 AN: 41426

American (AMR) AF: 0.169 AC: 2576 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5168

South Asian (SAS) AF: 0.0861 AC: 414 AN: 4810

European-Finnish (FIN) AF: 0.172 AC: 1813 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5744 AN: 67980

Other (OTH) AF: 0.128 AC: 271 AN: 2110

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
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs17102387; hg19: chr10-123416578;