rs5756069

Variant names:

• chr22-36052763-C-T
• rs5756069

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 0.293 in 152,190 control chromosomes in the GnomAD database, including 12,222 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 0.29 (12222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.293 AC: 44555 AN: 152072 Hom.: 12175 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.293 AC: 44659 AN: 152190 Hom.: 12222 Cov.: 32 AF XY: 0.283 AC XY: 21095 AN XY: 74418

African (AFR) AF: 0.732 AC: 30390 AN: 41494

American (AMR) AF: 0.147 AC: 2249 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.0855 AC: 443 AN: 5184

South Asian (SAS) AF: 0.134 AC: 645 AN: 4828

European-Finnish (FIN) AF: 0.0984 AC: 1043 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8866 AN: 68010

Other (OTH) AF: 0.230 AC: 487 AN: 2116

Alfa AF: 0.172 Hom.: 2094

Bravo AF: 0.317

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs5756069; hg19: chr22-36448811;