rs1545169

Variant names:

• chr5-111063678-T-G
• rs1545169

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 0.112 in 152,186 control chromosomes in the GnomAD database, including 1,475 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 0.11 (1475 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 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: 0.112 AC: 16999 AN: 152068 Hom.: 1476 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.112 AC: 17005 AN: 152186 Hom.: 1475 Cov.: 31 AF XY: 0.116 AC XY: 8643 AN XY: 74418

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0629 Hom.: 1032

Bravo AF: 0.116

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545169; hg19: chr5-110399376;