rs1154473

Positions:

• chr4-99438755-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;