rs1154473

Variant names:

• chr4-99438755-A-G
• rs1154473

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 0.594 in 150,756 control chromosomes in the GnomAD database, including 26,927 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 0.59 (26927 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.594 AC: 89411 AN: 150638 Hom.: 26904 Cov.: 27

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.594 AC: 89493 AN: 150756 Hom.: 26927 Cov.: 27 AF XY: 0.599 AC XY: 44017 AN XY: 73488

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.580

Alfa AF: 0.610 Hom.: 7166

Bravo AF: 0.585

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154473; hg19: chr4-100359912;