rs5748307

Variant names:

• chr22-19578209-G-A
• rs5748307

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 0.167 in 152,130 control chromosomes in the GnomAD database, including 3,381 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 0.17 (3381 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

ACMG classification

Verdict is Benign. Variant got -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 = 0.361 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: 0.167 AC: 25381 AN: 152012 Hom.: 3365 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.167 AC: 25424 AN: 152130 Hom.: 3381 Cov.: 32 AF XY: 0.165 AC XY: 12251 AN XY: 74370

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0997 Hom.: 1349

Bravo AF: 0.178

Asia WGS AF: 0.143 AC: 498 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	0.56
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5748307; hg19: chr22-19565732;