chr22-48105541-A-C

Variant names:

• chr22-48105541-A-C
• rs5768355

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 0.488 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.399 AC: 16521 AN: 41364

American (AMR) AF: 0.559 AC: 8525 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2671 AN: 5136

South Asian (SAS) AF: 0.571 AC: 2742 AN: 4800

European-Finnish (FIN) AF: 0.415 AC: 4379 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35764 AN: 67928

Other (OTH) AF: 0.496 AC: 1042 AN: 2102

Alfa AF: 0.524 Hom.: 36985

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs5768355; hg19: chr22-48501358;