rs4821467

Positions:

• chr22-36220154-G-A
• chr22-36220154-G-T

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 0.15 in 152,166 control chromosomes in the GnomAD database, including 2,942 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 0.15 (2942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.150 AC: 22864 AN: 152048 Hom.: 2939 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.150 AC: 22875 AN: 152166 Hom.: 2942 Cov.: 32 AF XY: 0.147 AC XY: 10958 AN XY: 74418

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.0771

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0591

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0369

Gnomad4 NFE AF: 0.0717

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0740 Hom.: 301

Bravo AF: 0.161

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821467; hg19: chr22-36616200;