rs1669748

Variant names:

• chr5-4921277-A-G
• rs1669748

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 0.741 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.876 AC: 36356 AN: 41510

American (AMR) AF: 0.679 AC: 10375 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2303 AN: 3472

East Asian (EAS) AF: 0.134 AC: 695 AN: 5176

South Asian (SAS) AF: 0.516 AC: 2491 AN: 4824

European-Finnish (FIN) AF: 0.691 AC: 7298 AN: 10562

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50705 AN: 67994

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.737 Hom.: 38419

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1669748; hg19: chr5-4921390;