rs884289

Variant names:

• chr10-2672557-A-G
• rs884289

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 0.123 in 152,234 control chromosomes in the GnomAD database, including 1,595 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 0.12 (1595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

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 = 0.235 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: 0.123 AC: 18710 AN: 152116 Hom.: 1586 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.123 AC: 18734 AN: 152234 Hom.: 1595 Cov.: 33 AF XY: 0.128 AC XY: 9542 AN XY: 74426

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0667 Hom.: 1082

Bravo AF: 0.128

Asia WGS AF: 0.193 AC: 674 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	0.65
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884289; hg19: chr10-2714749; COSMIC: COSV61308365;