rs223889

chr16-57358329-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047434449.1(CCL22):c.9+181T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,070 control chromosomes in the GnomAD database, including 28,951 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 0.59 (28951 hom., cov: 32)
• Consequence: CCL22 XM_047434449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

CCL22 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL22	XM_047434449.1	c.9+181T>C		intron_variant
CCL22	XM_047434450.1	c.-31+397T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89792 AN: 151952 Hom.: 28938 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.591 AC: 89842 AN: 152070 Hom.: 28951 Cov.: 32 AF XY: 0.591 AC XY: 43951 AN XY: 74354

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.633

Alfa AF: 0.677 Hom.: 6073

Bravo AF: 0.568

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.47
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223889; hg19: chr16-57392241;