rs1875473

chr5-154480744-C-Achr5-154480744-C-T

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 0.118 in 152,212 control chromosomes in the GnomAD database, including 1,144 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 0.12 (1144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17919 AN: 152094 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.118 AC: 17939 AN: 152212 Hom.: 1144 Cov.: 32 AF XY: 0.115 AC XY: 8564 AN XY: 74410

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.109

Alfa AF: 0.127 Hom.: 819

Bravo AF: 0.116

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	4.6
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1875473; hg19: chr5-153860304;