rs135556

chr22-46147582-T-Cchr22-46147582-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 0.326 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;