rs2199922

Variant names:

• chr8-135232083-C-T
• rs2199922

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0695 in 152,262 control chromosomes in the GnomAD database, including 513 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 0.069 (513 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0969 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: 0.0696 AC: 10583 AN: 152144 Hom.: 512 Cov.: 33

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0695 AC: 10577 AN: 152262 Hom.: 513 Cov.: 33 AF XY: 0.0682 AC XY: 5077 AN XY: 74444

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0901 Hom.: 962

Bravo AF: 0.0661

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	11
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2199922; hg19: chr8-136244326;