rs1669748

Variant names:

• chr5-4921277-A-G
• rs1669748

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 0.741 in 152,142 control chromosomes in the GnomAD database, including 43,310 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 0.74 (43310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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: 0.741 AC: 112611 AN: 152024 Hom.: 43263 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.741 AC: 112724 AN: 152142 Hom.: 43310 Cov.: 32 AF XY: 0.730 AC XY: 54307 AN XY: 74370

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.723

Alfa AF: 0.736 Hom.: 28059

Bravo AF: 0.743

Asia WGS AF: 0.393 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1669748; hg19: chr5-4921390;