rs884289

Variant names:

• chr10-2672557-A-G
• rs884289

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 0.123 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.218 AC: 9056 AN: 41518

American (AMR) AF: 0.149 AC: 2280 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5172

South Asian (SAS) AF: 0.138 AC: 667 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1519 AN: 10618

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3570 AN: 68014

Other (OTH) AF: 0.100 AC: 211 AN: 2110

Alfa AF: 0.0762 Hom.: 2294

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

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