rs17321444

Variant names:

• chr2-22885244-C-T
• rs17321444

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 0.101 in 152,184 control chromosomes in the GnomAD database, including 880 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 0.10 (880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.127 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: 0.101 AC: 15313 AN: 152066 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.101 AC: 15330 AN: 152184 Hom.: 880 Cov.: 32 AF XY: 0.0980 AC XY: 7288 AN XY: 74404

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0304

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.125

Alfa AF: 0.121 Hom.: 1603

Bravo AF: 0.106

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17321444; hg19: chr2-23108116;