22-27456222-T-C

Variant names:

• chr22-27456222-T-C
• rs6005451

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0947 in 152,204 control chromosomes in the GnomAD database, including 679 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 0.095 (679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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: 0.0948 AC: 14413 AN: 152086 Hom.: 680 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0947 AC: 14409 AN: 152204 Hom.: 679 Cov.: 32 AF XY: 0.0928 AC XY: 6907 AN XY: 74418

African (AFR) AF: 0.0679 AC: 2819 AN: 41524

American (AMR) AF: 0.0860 AC: 1315 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.0965 AC: 500 AN: 5180

South Asian (SAS) AF: 0.144 AC: 696 AN: 4822

European-Finnish (FIN) AF: 0.0768 AC: 813 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7564 AN: 68012

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.107 Hom.: 4148

Bravo AF: 0.0917

Asia WGS AF: 0.115 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs6005451; hg19: chr22-27852183; COSMIC: COSV71131613;