rs5768355

Positions:

• chr22-48105541-A-C

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 0.488 in 151,798 control chromosomes in the GnomAD database, including 18,431 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 0.49 (18431 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 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: 0.488 AC: 74026 AN: 151680 Hom.: 18404 Cov.: 30

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.488 AC: 74101 AN: 151798 Hom.: 18431 Cov.: 30 AF XY: 0.483 AC XY: 35839 AN XY: 74176

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.496

Alfa AF: 0.527 Hom.: 28466

Bravo AF: 0.490

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5768355; hg19: chr22-48501358;