rs5756379

chr22-36879862-C-T

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 0.565 in 152,052 control chromosomes in the GnomAD database, including 26,173 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 0.57 (26173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.566 AC: 85922 AN: 151934 Hom.: 26165 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.565 AC: 85943 AN: 152052 Hom.: 26173 Cov.: 32 AF XY: 0.569 AC XY: 42335 AN XY: 74354

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.580

Alfa AF: 0.647 Hom.: 65170

Bravo AF: 0.544

Asia WGS AF: 0.639 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756379; hg19: chr22-37275904;