chr22-46147582-T-C

Variant names:

• chr22-46147582-T-C
• rs135556

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 0.326 in 152,040 control chromosomes in the GnomAD database, including 9,309 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 0.33 (9309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.326 AC: 49452 AN: 151920 Hom.: 9280 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.326 AC: 49532 AN: 152040 Hom.: 9309 Cov.: 32 AF XY: 0.319 AC XY: 23679 AN XY: 74322

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.305

Alfa AF: 0.316 Hom.: 1007

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.0050

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135556; hg19: chr22-46543485;