rs2073449

Positions:

• chr22-22196484-T-C
• chr22-22196484-T-G

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 0.179 in 152,098 control chromosomes in the GnomAD database, including 2,755 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 0.18 (2755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27186 AN: 151984 Hom.: 2755 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.179 AC: 27206 AN: 152098 Hom.: 2755 Cov.: 32 AF XY: 0.186 AC XY: 13839 AN XY: 74364

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.152

Alfa AF: 0.172 Hom.: 3298

Bravo AF: 0.178

Asia WGS AF: 0.201 AC: 697 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.71
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: rs2073449; hg19: chr22-22550884;