rs5748307

Variant names:

• chr22-19578209-G-A
• rs5748307

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 0.167 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
• Publications: 8 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 = 0.361 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

African (AFR) AF: 0.366 AC: 15180 AN: 41460

American (AMR) AF: 0.109 AC: 1671 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3470

East Asian (EAS) AF: 0.134 AC: 698 AN: 5190

South Asian (SAS) AF: 0.159 AC: 767 AN: 4828

European-Finnish (FIN) AF: 0.0458 AC: 485 AN: 10592

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0861 AC: 5854 AN: 67992

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.107 Hom.: 2098

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs5748307; hg19: chr22-19565732;