rs5766305

Variant names:

• chr22-45019531-T-C
• rs5766305

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 0.162 in 152,128 control chromosomes in the GnomAD database, including 2,119 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 0.16 (2119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 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: 0.162 AC: 24613 AN: 152010 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.162 AC: 24649 AN: 152128 Hom.: 2119 Cov.: 32 AF XY: 0.160 AC XY: 11872 AN XY: 74374

African (AFR) AF: 0.152 AC: 6312 AN: 41504

American (AMR) AF: 0.134 AC: 2041 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3468

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4812

European-Finnish (FIN) AF: 0.126 AC: 1342 AN: 10612

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12664 AN: 67954

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.178 Hom.: 9481

Bravo AF: 0.160

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs5766305; hg19: chr22-45415412;