rs1663689

chr10-8983232-T-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 0.251 in 152,034 control chromosomes in the GnomAD database, including 5,126 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 0.25 (5126 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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: 0.251 AC: 38159 AN: 151916 Hom.: 5110 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.251 AC: 38217 AN: 152034 Hom.: 5126 Cov.: 31 AF XY: 0.251 AC XY: 18629 AN XY: 74316

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.245

Alfa AF: 0.232 Hom.: 704

Bravo AF: 0.261

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1663689; hg19: chr10-9025195;